Network biologyLarge-scale biomedical data and text mining

Lars Juhl Jensen

three parts

one thing in common

guilt by association

Part 1protein networks

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

>1100 genomes

genomic context

gene fusion

Korbel et al., Nature Biotechnology, 2004

experimental data

Jensen & Bork, Science, 2008

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences, 2008

many data types

many databases

different formats

different identifiers

variable quality

quality scores

von Mering et al., Nucleic Acids Research, 2005

calibrate vs. gold standard

von Mering et al., Nucleic Acids Research, 2005

orthology transfer

Part 2literature mining

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

identify the concepts

proteins

compartments

tissues

diseases

comprehensive lexicon

orthographic variation

“black list”

information extraction

co-mentioning

http://diseases.jensenlab.org

abstracts

restricted full-text access

collaborate with publishers

Part 3medical informatics

electronic health records

Jensen et al., Nature Reviews Genetics, 2012

structured data

Jensen et al., Nature Reviews Genetics, 2012

unstructured data

in Danish

by busy doctors

about psychiatric patients

comorbidity

Jensen et al., Nature Reviews Genetics, 2012

multiple testing

Roque et al., PLoS Computational Biology, 2011

patient clustering

Roque et al., PLoS Computational Biology, 2011

cluster characterization

Roque et al., PLoS Computational Biology, 2011

temporal correlation

medication

adverse drug events

pharmacovigilance

Acknowledgments

EPR miningFrancisco S Roque

Peter B Jensen

Robert Eriksson

Henriette Schmock

Marlene Dalgaard

Massimo Andreatta

Thomas Hansen

Karen Søeby

Søren Bredkjær

Anders Juul

Thomas Werge

Søren Brunak

STRINGDamian Szklarczyk

Andrea Franceschini

Michael Kuhn

Milan Simonovic

Alexander Roth

Pablo Minguez

Tobias Doerks

Manuel Stark

Jean Muller

Peer Bork

Christian von Mering

Text miningSune Frankild

Heiko Horn

Evangelos Pafilis

Janos Binder

Reinhardt Schneider

Sean O’Donoghue

larsjuhljensen

Thank you