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Network biology: Large-scale data integration and text mining

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Lars Juhl Jensen
Lars Juhl Jensen
Tecnología
1 de 69
Network biology Large-scale data integration and text mining Lars Juhl Jensen
academic research center
contract research
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
species
Pafilis et al., PLOS ONE, 2013
environments
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 Lucia Fanini Sarah Faulwetter Christina Pavloudi Aikaterini Vasileiadou Janos Binder Michael Kuhn Nigel Brown Christos Arvanitidis Reinhardt Schneider Sean O’Donoghue
Network biology: Large-scale data integration and text mining

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