Network biologyLarge-scale data and text

mining

Lars Juhl Jensen

association networks

guilt by association

biological systems

protein networks

STRING

1100+ genomes

computational predictions

gene fusion

Korbel et al., Nature Biotechnology, 2004

gene neighborhood

Korbel et al., Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology, 2004

experimental data

gene coexpression

protein interactions

Jensen & Bork, Science, 2008

curated knowledge

complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

not same species

hard work

(Ph.D. students)

common identifiers

quality scores

von Mering et al., Nucleic Acids Research, 2005

score calibration

von Mering et al., Nucleic Acids Research, 2005

homology-based transfer

Franceschini et al., Nucleic Acids Research, 2013

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

cyclin dependent kinase 1

expansion rules

hCdc2

CDC2

flexible matching

cyclin-dependent kinase 1

cyclin dependent kinase 1

“black list”

SDS

co-mentioning

counting

within documents

within paragraphs

within sentences

natural language processing

Gene and protein namesCue words for entity recognitionVerbs for relation extraction

[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]

text corpus

~2 million full-text articles

~22 million abstracts

wait there’s more

general approach

curated knowledge

experimental data

text mining

computational predictions

common identifiers

quality scores

score calibration

visualization

protein networks

string-db.org

chemical networks

stitch-db.org

subcellular localization

compartments.jensenlab.org

tissue expression

tissues.jensenlab.org

temporal expression

de Lichtenberg, Jensen et al., Science, 2005

disease associations

medical informatics

electronic health records

drugs

side effects

biodiversity informatics

British Heritage Library

organisms

environments

AcknowledgmentsSTRING and

STITCHMichael Kuhn

Damian SzklarczykAndrea Franceschini

Milan SimonovicAlexander RothSune Pletscher-

FrankildJianyi Lin

Pablo MinguezChristian von Mering

Peer Bork

Localization and diseaseSune Pletscher-FrankildAlberto SantosJanos BinderKalliopi TsafouChristian StolteAlbert PallejaHeiko HornEvangelos PafilisReinhardt SchneiderSean O’ Donoghue