network biology: large-scale data integration and text mining

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