one tagger, many uses - illustrating the power of ontologies in named entity recognition

Lars Juhl Jensen

One tagger, many usesIllustrating the power of ontologies in named

entity recognition

C++ tagger

flexible matching

>1000 abstracts / second

inherently thread-safe

comprehensive dictionary

expansion rules

curated blacklist

80–90% precision

70–80% recall

molecular entities

genes/proteins

chemicals

biomedical literature

assess studiedness

association networks

co-occurrence

data integration

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

Kuhn et al., Nucleic Acids Research, 2016stitch-db.org

localization & expression

GO cellular component

Brenda Tissue Ontology

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

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

diseases & side effects

Disease Ontology

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

MedDRA

FDA product labels

Kuhn et al., Nucleic Acids Research, 2016sideeffects.embl.de

Danish dictionaries

electronic medical records

post-market monitoring

organisms & habitats

NCBI Taxonomy

BioNLP shared task

Environment Ontology

EOL descriptions

Pafilis et al., Bioinformatics, 2016environments.hcmr.gr / eol.org

interactive annotation

Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr

Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr

BioCreative V

AcknowledgmentsSune Pletscher-

FrankildEvangelos PafilisDamian Szklarczyk

Christian von MeringMichael KuhnPeer Bork

Robert ErikssonPeter Bjødstrup

JensenSøren Brunak