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STRING Protein networks from data and text mining Lars Juhl Jensen

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Page 1: STRING - Protein networks from data and text mining

STRINGProtein networks from data and

text mining

Lars Juhl Jensen

Page 2: STRING - Protein networks from data and text mining

9.6 million proteins

Page 3: STRING - Protein networks from data and text mining

functional associations

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genomic context

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gene fusion

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Korbel et al., Nature Biotechnology, 2004

Page 7: STRING - Protein networks from data and text mining

gene neighborhood

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Korbel et al., Nature Biotechnology, 2004

Page 9: STRING - Protein networks from data and text mining

phylogenetic profiles

Page 10: STRING - Protein networks from data and text mining

Korbel et al., Nature Biotechnology, 2004

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experimental data

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gene coexpression

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physical interactions

Page 15: STRING - Protein networks from data and text mining

Jensen & Bork, Science, 2008

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curated knowledge

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protein complexes

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Page 19: STRING - Protein networks from data and text mining

pathways

Page 20: STRING - Protein networks from data and text mining

Letunic & Bork, Trends in Biochemical Sciences, 2008

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many databases

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different formats

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different identifiers

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variable quality

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not comparable

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hard work

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parsers

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mapping files

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quality scores

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von Mering et al., Nucleic Acids Research, 2005

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score calibration

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von Mering et al., Nucleic Acids Research, 2005

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implicit weighting by quality

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common scale

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missing most of the data

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>10 km

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too much to read

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computer

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as smart as a dog

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teach it specific tricks

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Page 43: STRING - Protein networks from data and text mining

named entity recognition

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comprehensive lexicon

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cyclin dependent kinase 1

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CDC2

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orthographic variation

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spaces and hyphens

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cyclin dependent kinase 1

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cyclin-dependent kinase 1

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prefixes and suffixes

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CDC2

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hCdc2

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“black list”

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SDS

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co-mentioning

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counting

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within documents

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within paragraphs

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within sentences

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quality scores

Page 62: STRING - Protein networks from data and text mining

score calibration

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combine all evidence

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

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make it available

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web resource

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download files

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REST API

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Bioconductor package

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Cytoscape App

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AcknowledgmentsDamian Szklarczyk

Michael KuhnAndrea Franceschini

Milan SimonovicAlexander RothSune Pletscher-

FrankildJohn “Scooter”

MorrisChristian von

MeringPeer Bork


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