network biology: large-scale data integration and text mining
TRANSCRIPT
Network biologyLarge-scale data integration and text
mining
Lars Juhl Jensen
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
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 MeringDamian Szklarczyk
Michael KuhnManuel Stark
Samuel ChaffronChris Creevey
Jean MullerTobias DoerksPhilippe Julien
Alexander RothMilan Simonovic
Jan KorbelBerend Snel
Martijn HuynenPeer Bork
Literature miningSune FrankildEvangelos PafilisHeiko HornAlberto SantosKalliopi TsafouJanos BinderMichael KuhnNigel BrownReinhardt SchneiderSean O’Donoghue
ThanksTorun!
Janusz BujnickiWieslaw Nowak
Arne Elofsson
Wieslaw NowakWitold Rudnicki
Łukasz Pepłowski
Karolina Mikulska
Anna Gogolinska
Rafał Jakubowski
Marcin Dabrowski