![Page 1: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/1.jpg)
Network biologyLarge-scale data integration and text
mining
Lars Juhl Jensen
![Page 2: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/2.jpg)
association networks
![Page 3: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/3.jpg)
guilt by association
![Page 4: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/4.jpg)
![Page 5: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/5.jpg)
STRING
![Page 6: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/6.jpg)
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
![Page 7: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/7.jpg)
computational predictions
![Page 8: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/8.jpg)
gene fusion
![Page 9: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/9.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 10: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/10.jpg)
experimental data
![Page 11: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/11.jpg)
physical interactions
![Page 12: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/12.jpg)
Jensen & Bork, Science, 2008
![Page 13: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/13.jpg)
curated knowledge
![Page 14: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/14.jpg)
metabolic pathways
![Page 15: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/15.jpg)
Letunic & Bork, Trends in Biochemical Sciences, 2008
![Page 16: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/16.jpg)
many databases
![Page 17: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/17.jpg)
different formats
![Page 18: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/18.jpg)
different identifiers
![Page 19: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/19.jpg)
variable quality
![Page 20: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/20.jpg)
not comparable
![Page 21: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/21.jpg)
hard work
![Page 22: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/22.jpg)
quality scores
![Page 23: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/23.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 24: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/24.jpg)
calibrate vs. gold standard
![Page 25: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/25.jpg)
missing most of the data
![Page 26: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/26.jpg)
>10 km
![Page 27: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/27.jpg)
too much to read
![Page 28: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/28.jpg)
computer
![Page 29: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/29.jpg)
as smart as a dog
![Page 30: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/30.jpg)
teach it specific tricks
![Page 31: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/31.jpg)
![Page 32: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/32.jpg)
![Page 33: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/33.jpg)
named entity recognition
![Page 34: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/34.jpg)
comprehensive lexicon
![Page 35: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/35.jpg)
cyclin dependent kinase 1
![Page 36: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/36.jpg)
CDC2
![Page 37: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/37.jpg)
expansion rules
![Page 38: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/38.jpg)
CDC2
![Page 39: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/39.jpg)
hCdc2
![Page 40: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/40.jpg)
flexible matching
![Page 41: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/41.jpg)
cyclin dependent kinase 1
![Page 42: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/42.jpg)
cyclin-dependent kinase 1
![Page 43: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/43.jpg)
“black list”
![Page 44: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/44.jpg)
SDS
![Page 45: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/45.jpg)
count co-mentioning
![Page 46: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/46.jpg)
general approach
![Page 47: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/47.jpg)
small molecules
![Page 48: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/48.jpg)
Kuhn et al., Nucleic Acids Research, 2012
![Page 49: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/49.jpg)
compartments
![Page 50: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/50.jpg)
compartments.jensenlab.org
![Page 51: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/51.jpg)
tissues
![Page 52: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/52.jpg)
tissues.jensenlab.org
![Page 53: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/53.jpg)
diseases
![Page 54: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/54.jpg)
![Page 55: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/55.jpg)
evidence viewers
![Page 56: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/56.jpg)
![Page 57: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/57.jpg)
web services
![Page 58: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/58.jpg)
compartments.jensenlab.org
![Page 59: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/59.jpg)
download files
![Page 60: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/60.jpg)
Acknowledgments
Protein networks
Christian von MeringDamian Szklarczyk
Michael KuhnManuel Stark
Samuel ChaffronChris Creevey
Jean MullerTobias DoerksPhilippe Julien
Alexander RothMilan Simonovic
Jan KorbelBerend Snel
Martijn HuynenPeer Bork
Literature miningSune FrankildEvangelos PafilisHeiko HornAlberto SantosKalliopi TsafouJanos BinderMichael KuhnNigel BrownReinhardt SchneiderSean O’Donoghue
![Page 61: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/61.jpg)
![Page 62: Network biology: Large-scale data integration and text mining](https://reader036.vdocument.in/reader036/viewer/2022062418/554e8a14b4c90573338b49a7/html5/thumbnails/62.jpg)
ThanksTorun!
Janusz BujnickiWieslaw Nowak
Arne Elofsson
Wieslaw NowakWitold Rudnicki
Łukasz Pepłowski
Karolina Mikulska
Anna Gogolinska
Rafał Jakubowski
Marcin Dabrowski