network biology - large-scale data integration and text mining
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Network biologyLarge-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
AcknowledgmentsNetPhorestRune Linding
Martin Lee Miller
Erwin Schoof
Francesca Diella
Claus Jørgensen
Michele Tinti
Lei Li
Marilyn Hsiung
Sirlester A. Parker
Jennifer Bordeaux
Thomas Sicheritz-Pontén
Marina Olhovsky
Adrian Pasculescu
Jes Alexander
Stefan Knapp
Nikolaj Blom
Peer Bork
Shawn Li
Gianni Cesareni
Tony Pawson
Benjamin Turk
Michael Yaffe
Søren Brunak
STRINGChristian 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
Peer Bork
NetworKINRune Linding
Heiko Horn
Gerard Ostheimer
Martin Lee Miller
Francesca Diella
Karen Colwill
Jing Jin
Pavel Metalnikov
Vivian Nguyen
Adrian Pasculescu
Jin Gyoon Park
Leona D. Samson
Rob Russell
Peer Bork
Michael Yaffe
Tony Pawson
Text miningSune Frankild
Evangelos Pafilis
Janos Binder
Kalliopi Tsafou
Heiko Horn
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue
Questions?
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