data integration and visualization
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Lars Juhl Jensen
Data integration and visualization
protein networks
3+ years ahead
STRING
Huynen et al., Current Opinion in Structural Biology, 2000
genomic context
experimental data
text mining
~22 million abstracts
~4 million full-text articles
comprehensive lexicon
proteins
small molecules
compartments
tissues
diseases
organisms
environments
orthographics variation
flexible matching
hyphens and spaces
expansion rules
singular vs. plural
“black list”
relation extraction
count co-mentioning
within documents
within paragraphs
within sentences
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
payload
compartments.jensenlab.org
COMPARTMENTS
compartments.jensenlab.org
TISSUES
tissues.jensenlab.org
DISEASES
visualization
de Lichtenberg, Jensen et al., Science, 2005
Ciccarelli, Doerks et al., Science, 2006
von Mering et al., Science, 2007
Jensen & Bork, Science, 2008
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