Lars Juhl Jensen

Biomedical text miningand network analysis

why text mining?

data mining

unstructured text

too much to read

biomedical literature

>10 km

electronic medical records

in Danish

named entity recognition

comprehensive lexicon

diseases

drugs

adverse drug reactions

synonyms

Clozapine

Clozaril

kidney failure

renal failure

expansion rules

Clozapine

Clozapineclozapi

n

clossapin

klozapine

chlosapin

chlosapine

chlozapin

chlozapine

klossapin

closapine

klozapinklosapi

n

kidney failure

failure of kidney

EMR mining

detailed phenotyping

Roque et al., PLOS Computational Biology, 2011

3262638254947

Assigned codes

Text mined codes

comorbidity

Roque et al., PLOS Computational Biology, 2011

patient stratification

Roque et al., PLOS Computational Biology, 2011

pharmacovigilance

drugs

adverse drug events

temporal correlations

Eriksson et al., Drug Safety, 2014

Eriksson et al., Drug Safety, 2014

Eriksson et al., Drug Safety, 2014

Eriksson et al., Drug Safety, 2014

molecular networks

text mining

data mining

association networks

web resources

disease–gene associations

diseases.jensenlab.org Frankild et al., Methods, 2015

tissue expression

tissues.jensenlab.org Santos et al., PeerJ, 2015

subcellular localization

Binder et al., Database, 2014compartments.jensenlab.org

protein networks

Szklarczyk et al., Nucleic Acids Research, 2015string-db.org

chemical networks

stitch-db.org

questions?