Download - Network integration of data and text
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Network integration of data and text
Lars Juhl Jensen
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Part 1text mining
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>10 km
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exponential growth
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law of diminishing returns
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some things are constant
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~45 seconds per paper
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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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Reflect
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augmented browsing
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browser add-on
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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collaborations
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web services
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Utopia Documents
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information extraction
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co-mentioning
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<10 hours
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no access
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Part 2protein networks
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STRING
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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630 genomes
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many databases
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genomic context
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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conserved neighborhood
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operons
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Korbel et al., Nature Biotechnology, 2004
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bidirectional promoters
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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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physical interactions
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Jensen & Bork, Science, 2008
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gene coexpression
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curated knowledge
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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text mining
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many data types
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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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quality scores
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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orthology transfer
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Frishman et al., Modern Genome Annotation, 2009
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Part 3small molecule networks
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STITCH
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Kuhn et al., Nucleic Acids Research, 2010
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in vitro binding assays
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text mining
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chemical similarity
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Campillos & Kuhn et al., Science, 2008
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similar drugs share targets
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Campillos & Kuhn et al., Science, 2008
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only trivial predictions
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phenotypic similarity
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chemical perturbations
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phenotypic readouts
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drug treatment
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side effects
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no database
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package inserts
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Campillos & Kuhn et al., Science, 2008
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text mining
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manual validation
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side-effect correlations
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Campillos & Kuhn et al., Science, 2008
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side-effect frequencies
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Campillos & Kuhn et al., Science, 2008
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raw similarity score
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Campillos & Kuhn et al., Science, 2008
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p-values
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Campillos & Kuhn et al., Science, 2008
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side-effect similarity
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chemical similarity
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Campillos & Kuhn et al., Science, 2008
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drug–drug network
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Campillos & Kuhn et al., Science, 2008
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categorization
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Campillos & Kuhn et al., Science, 2008
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20 drug–drug pairs
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in vitro binding assays
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Ki<10 µM for 11 of 20
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cell assays
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9 of 9 showed activity
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Acknowledgments
ReflectSune Frankild
Heiko Horn
Evangelos Pafilis
Michael Kuhn
Reinhardt Schneider
Sean O’Donoghue
Side effectsMonica Campillos
Michael Kuhn
Anne-Claude Gavin
Peer Bork
STRING/STITCHDamian Szklarczyk
Andrea Franceschini
Michael Kuhn
Milan Simonovic
Alexander Roth
Pablo Minguez
Tobias Doerks
Manuel Stark
Jean Muller
Andreas Beyer
Peer Bork
Christian von Mering
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larsjuhljensen
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