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Network biology: Large-scale data integration and text mining
 

Network biology: Large-scale data integration and text mining

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    Network biology: Large-scale data integration and text mining Network biology: Large-scale data integration and text mining Presentation Transcript

    • Network biology Large-scale data integration and text mining Lars Juhl Jensen
    • association networks
    • guilt by association
    • STRING
    • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    • computational predictions
    • gene fusion
    • Korbel et al., Nature Biotechnology, 2004
    • experimental data
    • physical interactions
    • Jensen & Bork, Science, 2008
    • curated knowledge
    • metabolic pathways
    • Letunic & Bork, Trends in Biochemical Sciences, 2008
    • many databases
    • different formats
    • different identifiers
    • variable quality
    • not comparable
    • hard work
    • quality scores
    • von Mering et al., Nucleic Acids Research, 2005
    • calibrate vs. gold standard
    • missing most of the data
    • >10 km
    • too much to read
    • computer
    • as smart as a dog
    • teach it specific tricks
    • named entity recognition
    • comprehensive lexicon
    • cyclin dependent kinase 1
    • CDC2
    • expansion rules
    • CDC2
    • hCdc2
    • flexible matching
    • cyclin dependent kinase 1
    • cyclin-dependent kinase 1
    • “black list”
    • SDS
    • count co-mentioning
    • general approach
    • small molecules
    • Kuhn et al., Nucleic Acids Research, 2012
    • compartments
    • compartments.jensenlab.org
    • tissues
    • tissues.jensenlab.org
    • diseases
    • evidence viewers
    • web services
    • compartments.jensenlab.org
    • download files
    • Acknowledgments Protein networks Christian von Mering Damian Szklarczyk Michael Kuhn Manuel Stark Samuel Chaffron Chris Creevey Jean Muller Tobias Doerks Philippe Julien Alexander Roth Milan Simonovic Jan Korbel Berend Snel Martijn Huynen Literature mining Sune Frankild Evangelos Pafilis Heiko Horn Alberto Santos Kalliopi Tsafou Janos Binder Michael Kuhn Nigel Brown Reinhardt Schneider Sean O’Donoghue
    • Thanks Toruń! Janusz Bujnicki Wieslaw Nowak Arne Elofsson Wieslaw Nowak Witold Rudnicki Łukasz Pepłowski Karolina Mikulska Anna Gogolinská Rafał Jakubowski