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Network biologyLarge-scale data and text mining
Lars Juhl Jensen
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guilt by association
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protein networks
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STRING
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computational predictions
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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gene neighborhood
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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experimental data
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gene coexpression
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protein interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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complexes
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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not same species
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hard work
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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homology-based transfer
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Franceschini et al., Nucleic Acids Research, 2013
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missing most of the data
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text mining
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>10 km
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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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comprehensive lexicon
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CDC2
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cyclin dependent kinase 1
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expansion rules
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hCdc2
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CDC2
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flexible matching
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cyclin-dependent kinase 1
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cyclin dependent kinase 1
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“black list”
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SDS
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augmented browsing
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Reflect
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browser add-on
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real-time text mining
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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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information extraction
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co-mentioning
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within documents
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within paragraphs
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within sentences
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text corpus
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~22 million abstracts
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no access
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millions of full-text articles
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localization and disease
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general approach
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COMPARTMENTS
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TISSUES
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DISEASES
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curated knowledge
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experimental data
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text mining
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computational predictions
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common identifiers
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quality scores
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visualization
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compartments.jensenlab.org
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tissues.jensenlab.org
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dissemination
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web interfaces
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web services
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diseases.jensenlab.org
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bulk download
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AcknowledgmentsSTRING
Christian von Mering
Damian Szklarczyk
Michael KuhnManuel Stark
Samuel ChaffronChris Creevey
Jean MullerTobias DoerksPhilippe Julien
Alexander RothMilan Simonovic
Jan KorbelBerend Snel
Martijn HuynenPeer Bork
Text miningSune FrankildEvangelos PafilisKalliopi TsafouAlberto SantosJanos BinderHeiko HornMichael KuhnNigel BrownReinhardt SchneiderSean O’ Donoghue