Data integration and visualization

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