biomedical text mining and network analysis
TRANSCRIPT
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?