Literature mining: what is it, and should I care?
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Literature mining: what is it, and should I care?

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EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 10, 2008

EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 10, 2008

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    Literature mining: what is it, and should I care? Literature mining: what is it, and should I care? Presentation Transcript

    • Literature mining
    • Explosion
    • exponential increase
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    • some things never change
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    • “ graph calculus”
    • =
    • ~50 seconds per paper
    • Information retrieval
    • find the relevant papers
    • ad hoc retrieval
    • user-specified query
    • “ yeast AND cell cycle”
    • stemming
    • yeast / yeasts
    • dynamic query expansion
    • yeast / S. cerevisiae
    • ranking
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    • Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation
    • no tool will find it
    • Entity recognition
    • identify the substance(s)
    • Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
    • good synonyms list
    • orthographic variation
    • CDC28
    • Cdc28p
    • disambiguation
    • Cdc2
    • APC
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    • still too much to read
    • Information extraction
    • formalize the facts
    • co-mentioning
    • NLP Natural Language Processing
    • Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
    • database
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    • integration
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    • STRING & STITCH
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    • Acknowledgments
      • STRING & STITCH
        • Christian von Mering
        • Michael Kuhn
        • Manuel Stark
        • Samuel Chaffron
        • Philippe Julien
        • Tobias Doerks
        • Jan Korbel
        • Berend Snel
        • Martijn Huynen
        • Peer Bork
        • The movie “Brazil”
      • Reflect
        • Evangelos Pafilis
        • Michael Kuhn
        • Heiko Horn
        • Peer Bork
        • Sean O’Donoghue
        • Reinhardt Schneider
      • NLP pipeline
        • Jasmin Saric
        • Rossitza Ouzounova
        • Isabel Rojas
        • Peer Bork