the string database and related tools

The STRING database and related tools

Lars Juhl Jensen

association networks

guilt by association

molecular networks

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

protein interactions

Jensen & Bork, Science, 2008

gene coexpression

curated knowledge

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

not same species

hard work

scoring schemes

von Mering et al., Nucleic Acids Research, 2005

score calibration

gold standard

von Mering et al., Nucleic Acids Research, 2005

orthology-based transfer

Franceschini et al., Nucleic Acids Research, 2013

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

CDC2

cyclin dependent kinase 1

orthographic variation

expansion rules

CDC2

hCdc2

flexible matching

cyclin dependent kinase 1

cyclin-dependent kinase 1

“black list”

SDS

information extraction

co-mentioning

counting

within documents

within paragraphs

within sentences

scoring scheme

score calibration

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]

general approach

computational predictions

experimental data

curated knowledge

text mining

common identifiers

quality scores

score calibration

visualization

web resource

STRING

protein networks

string-db.org

STITCH

chemical networks

stitch-db.org

COMPARTMENTS

subcellular localization

compartments.jensenlab.org

TISSUES

tissue expression

tissues.jensenlab.org

DISEASES

disease associations

AcknowledgmentsSTRING and STITCH

Michael KuhnDamian Szklarczyk

Andrea 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