STRING Protein networks from data and text mining

STRING Protein networks from data and text mining Lars Juhl Jensen

9. 6 million proteins

functional associations

guilt by association

genomic context

gene fusion

Korbel et al. , Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al. , Nature Biotechnology, 2004

experimental data

gene coexpression

physical interactions

Jensen & Bork, Science, 2008

curated knowledge

protein complexes

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

hard work

parsers

mapping files

quality scores

von Mering et al. , Nucleic Acids Research, 2005

score calibration

von Mering et al. , Nucleic Acids Research, 2005

implicit weighting by quality

common scale

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

CDC 2

orthographic variation

spaces and hyphens

cyclin dependent kinase 1

cyclin-dependent kinase 1

prefixes and suffixes

CDC 2

h. Cdc 2

“black list”

SDS

co-mentioning

counting

within documents

within paragraphs

within sentences

quality scores

score calibration

integration

visualization

string-db. org Szklarczyk et al. , Nucleic Acids Research, 2015

web resource

download files

REST API

Bioconductor package

Cytoscape App

protein query

disease query

Acknowledgments Damian Szklarczyk John "Scooter" Morris Helen Cook Michael Kuhn Stefan Wyder Milan Simonovic Alberto Santos Nadezhda Doncheva Alexander Roth Peer Bork Christian von Mering