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 biologyLarge-scale data integration and text mining Lars Juhl Jensen
    • three parts
    • signaling networks
    • association networks
    • text mining
    • signaling networks
    • proteomics
    • in vivo PTMs
    • actors are unknown
    • sequence specificity
    • Miller, Jensen et al., Science Signaling, 2008
    • no context
    • complexes
    • NetworKIN
    • Linding, Jensen, Ostheimer et al., Cell, 2007
    • association network
    • STRING
    • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    • computational predictions
    • gene fusion
    • Korbel et al., Nature Biotechnology, 2004
    • experimental data
    • Jensen & Bork, Science, 2008
    • curated knowledge
    • 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
    • text mining
    • >10 km
    • too much to read
    • computer
    • as smart as a dog
    • teach it specific tricks
    • named entity recognition
    • comprehensive lexicon
    • CDC2 = CDK1
    • orthographic variation
    • hCdc2
    • “black list”
    • SDS
    • information extraction
    • co-mentioning
    • quality scores
    • proteins
    • compartments
    • compartments.jensenlab.org
    • compartments.jensenlab.org
    • tissues
    • tissues.jensenlab.org
    • tissues.jensenlab.org
    • diseases
    • diseases.jensenlab.org
    • AcknowledgmentsNetPhorest NetworKIN STRING Text miningRune Linding Rune Linding Christian von Mering Sune FrankildMartin Lee Miller Heiko Horn Damian Szklarczyk Evangelos PafilisErwin Schoof Gerard Ostheimer Michael Kuhn Janos BinderFrancesca Diella Martin Lee Miller Manuel Stark Kalliopi TsafouClaus Jørgensen Francesca Diella Samuel Chaffron Heiko HornMichele Tinti Karen Colwill Chris Creevey Michael KuhnLei Li Jing Jin Jean Muller Nigel BrownMarilyn Hsiung Pavel Metalnikov Tobias Doerks Reinhardt SchneiderSirlester A. Parker Vivian Nguyen Philippe Julien Sean O’DonoghueJennifer Bordeaux Adrian Pasculescu Alexander RothThomas Sicheritz-Pontén Jin Gyoon Park Milan SimonovicMarina Olhovsky Leona D. Samson Jan KorbelAdrian Pasculescu Rob Russell Berend SnelJes Alexander Peer Bork Martijn HuynenStefan Knapp Michael Yaffe Peer BorkNikolaj Blom Tony PawsonPeer BorkShawn LiGianni CesareniTony PawsonBenjamin TurkMichael YaffeSøren Brunak
    • Questions?