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?