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Cellular Network Biology: Large-scale integration of data and text

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Lars Juhl Jensen
Lars Juhl Jensen

Cellular Network Biology: Large-scale integration of data and text

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Lars Juhl Jensen Cellular Network Biology Large-scale integration of data and text
community resources
text mining
Cytoscape App
software demo
community resources
STRING
protein networks
string-db.org
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
genomic context
experimental data
von Mering et al., Nucleic Acids Research, 2005
calibrated quality scores
von Mering et al., Nucleic Acids Research, 2005
RAIN
ncRNA networks
Junge, Refsgaard & Garde et al., Database, 2017
STITCH
chemical networks
Kuhn et al., Nucleic Acids Research, 2016stitch-db.org
drug databases
high-throughput screens
COMPARTMENTS
subcellular localization
Binder et al., Database, 2014compartments.jensenlab.org
GO annotations
sequence-based prediction
TISSUES
tissue expression
tissues.jensenlab.org Santos et al., PeerJ, 2015 Palasca & Santos et al., submitted, 2017
expression atlases
Palasca & Santos et al., submitted, 2017 Human HPA RNA−seq Human RNA−seq atlas Human GNF Human Exon Array Pig RNA−seq WUR Pig RNA−seq Aarhus Pig Array Rat RNA−seq BodyMap Rat RNA−seq MIT Rat Array Mouse RNA−seq MIT Mouse RNA−seq Encode Mouse GNF V3 Mouse GNF Heart Intestine Kidney Liver Nervoussystem Muscle Lung Spleen Lymphnode Pancreas Skin Stomach Thyroidgland Bonemarrow Saliva Adrenalgland Urine Blood Eye Gallbladder Bone MouseRatPigHuman
DISEASES
disease associations
diseases.jensenlab.org Frankild et al., Methods, 2015
curated knowledge
missing most of the data
text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
dictionary
genes/proteins
chemicals
cellular compartments
tissues
diseases
synonyms
cyclin dependent kinase 1
CDC2
orthographic variation
cyclin dependent kinase 1
cyclin-dependent kinase 1
CDC2
hCdc2
“black list”
SDS
co-mentioning
scoring scheme
open source
highly efficient
broadly applicable
Cytoscape
networks
tables
visual styles
stringApp
import from STRING
protein query
PubMed query
disease query
subcellular localization
tissue expression
enrichment analysis
Thank you STRING & STITCH Damian Szklarczyk Nadezhda Donche va John "Scooter" Morris Helen Cook Michael Kuhn Stefan Wyder Milan Simonovic Alexander Roth Peer Bork Christian von Merin g COMPARTMENTS, TISSUES & DISEASES Alberto Santos Oana Palasca Sune Pletscher- Frankild Christian Stolte Janos Binder Kalliopi Tsafou Jan Gorodkin Sean I. O’Donoghue RAIN Alexander Junge Jan C. Refsgaard Christian Garde Xiaoyong Pan Alberto Santos Ferhat Alkan Christian Anthon Christian von Meri ng Christopher Workman Jan Gorodkin

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