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Network biology: Large-scale data integration and text mining

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Lars Juhl Jensen
Lars Juhl Jensen
1 of 65
Network biology Large-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
Acknowledgments NetPhorest NetworKIN STRING Text mining Rune Linding Rune Linding Christian von Mering Sune Frankild Martin Lee Miller Heiko Horn Damian Szklarczyk Evangelos Pafilis Erwin Schoof Gerard Ostheimer Michael Kuhn Janos Binder Francesca Diella Martin Lee Miller Manuel Stark Kalliopi Tsafou Claus Jørgensen Francesca Diella Samuel Chaffron Heiko Horn Michele Tinti Karen Colwill Chris Creevey Michael Kuhn Lei Li Jing Jin Jean Muller Nigel Brown Marilyn Hsiung Pavel Metalnikov Tobias Doerks Reinhardt Schneider Sirlester A. Parker Vivian Nguyen Philippe Julien Sean O’Donoghue Jennifer Bordeaux Adrian Pasculescu Alexander Roth Thomas Sicheritz-Pontén Jin Gyoon Park Milan Simonovic Marina Olhovsky Leona D. Samson Jan Korbel Adrian Pasculescu Rob Russell Berend Snel Jes Alexander Peer Bork Martijn Huynen Stefan Knapp Michael Yaffe Peer Bork Nikolaj Blom Tony Pawson Peer Bork Shawn Li Gianni Cesareni Tony Pawson Benjamin Turk Michael Yaffe Søren Brunak
Questions?

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Network biology: Large-scale data integration and text mining

Editor's Notes

  1. Integration Automation Collaboration