Network biology - Large-scale data integration and text mining
-
Upload
lars-juhl-jensen -
Category
Documents
-
view
462 -
download
1
Transcript of Network biology - Large-scale data integration and text mining
![Page 1: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/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://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/2.jpg)
three parts
![Page 3: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/3.jpg)
signaling networks
![Page 4: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/4.jpg)
association networks
![Page 5: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/5.jpg)
text mining
![Page 6: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/6.jpg)
signaling networks
![Page 7: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/7.jpg)
proteomics
![Page 8: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/8.jpg)
in vivo PTMs
![Page 9: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/9.jpg)
actors are unknown
![Page 10: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/10.jpg)
sequence specificity
![Page 11: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/11.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 12: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/12.jpg)
no context
![Page 13: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/13.jpg)
complexes
![Page 14: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/14.jpg)
NetworKIN
![Page 15: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/15.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 16: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/16.jpg)
association network
![Page 17: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/17.jpg)
STRING
![Page 18: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/18.jpg)
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
![Page 19: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/19.jpg)
computational predictions
![Page 20: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/20.jpg)
gene fusion
![Page 21: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/21.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 22: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/22.jpg)
experimental data
![Page 23: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/23.jpg)
Jensen & Bork, Science, 2008
![Page 24: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/24.jpg)
curated knowledge
![Page 25: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/25.jpg)
Letunic & Bork, Trends in Biochemical Sciences, 2008
![Page 26: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/26.jpg)
many databases
![Page 27: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/27.jpg)
different formats
![Page 28: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/28.jpg)
different identifiers
![Page 29: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/29.jpg)
variable quality
![Page 30: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/30.jpg)
not comparable
![Page 31: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/31.jpg)
hard work
![Page 32: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/32.jpg)
quality scores
![Page 33: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/33.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 34: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/34.jpg)
calibrate vs. gold standard
![Page 35: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/35.jpg)
missing most of the data
![Page 36: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/36.jpg)
text mining
![Page 37: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/37.jpg)
>10 km
![Page 38: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/38.jpg)
too much to read
![Page 39: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/39.jpg)
computer
![Page 40: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/40.jpg)
as smart as a dog
![Page 41: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/41.jpg)
teach it specific tricks
![Page 42: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/42.jpg)
![Page 43: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/43.jpg)
![Page 44: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/44.jpg)
named entity recognition
![Page 45: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/45.jpg)
comprehensive lexicon
![Page 46: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/46.jpg)
CDC2 = CDK1
![Page 47: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/47.jpg)
orthographic variation
![Page 48: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/48.jpg)
hCdc2
![Page 49: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/49.jpg)
“black list”
![Page 50: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/50.jpg)
SDS
![Page 51: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/51.jpg)
information extraction
![Page 52: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/52.jpg)
co-mentioning
![Page 53: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/53.jpg)
![Page 54: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/54.jpg)
quality scores
![Page 55: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/55.jpg)
proteins
![Page 56: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/56.jpg)
compartments
![Page 57: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/57.jpg)
compartments.jensenlab.org
![Page 58: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/58.jpg)
compartments.jensenlab.org
![Page 59: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/59.jpg)
tissues
![Page 60: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/60.jpg)
tissues.jensenlab.org
![Page 61: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/61.jpg)
tissues.jensenlab.org
![Page 62: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/62.jpg)
diseases
![Page 63: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/63.jpg)
diseases.jensenlab.org
![Page 64: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/64.jpg)
AcknowledgmentsNetPhorestRune Linding
Martin Lee Miller
Erwin Schoof
Francesca Diella
Claus Jørgensen
Michele Tinti
Lei Li
Marilyn Hsiung
Sirlester A. Parker
Jennifer Bordeaux
Thomas Sicheritz-Pontén
Marina Olhovsky
Adrian Pasculescu
Jes Alexander
Stefan Knapp
Nikolaj Blom
Peer Bork
Shawn Li
Gianni Cesareni
Tony Pawson
Benjamin Turk
Michael Yaffe
Søren Brunak
STRINGChristian von Mering
Damian Szklarczyk
Michael Kuhn
Manuel Stark
Samuel Chaffron
Chris Creevey
Jean Muller
Tobias Doerks
Philippe Julien
Alexander Roth
Milan Simonovic
Jan Korbel
Berend Snel
Martijn Huynen
Peer Bork
NetworKINRune Linding
Heiko Horn
Gerard Ostheimer
Martin Lee Miller
Francesca Diella
Karen Colwill
Jing Jin
Pavel Metalnikov
Vivian Nguyen
Adrian Pasculescu
Jin Gyoon Park
Leona D. Samson
Rob Russell
Peer Bork
Michael Yaffe
Tony Pawson
Text miningSune Frankild
Evangelos Pafilis
Janos Binder
Kalliopi Tsafou
Heiko Horn
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue
![Page 65: Network biology - Large-scale data integration and text mining](https://reader035.fdocuments.in/reader035/viewer/2022062513/554e9287b4c90526358b4f0e/html5/thumbnails/65.jpg)
Questions?