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Tagger: Rapid dictionary-based named entity recognition

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Lars Juhl Jensen
Lars Juhl Jensen

Tagger: Rapid dictionary-based named entity recognition

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Lars Juhl Jensen Tagger Rapid dictionary-based named entity recognition
C++ engine
flexible matching
>1000 abstracts / second
inherently thread-safe
comprehensive dictionary
70–80% recall
expansion rules
80–90% precision
curated blacklist
entity types & use cases
genes/proteins
assess studiedness
Cannon et al., Bioinformatics, 2017newdrugtargets.org
construct networks
string-db.org Szklarczyk et al., Nucleic Acids Research, 2017
chemicals
cellular components
tissues
diseases
organisms
environments
interactive annotation
Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr
real-time tagger
BeCalm API
Python wrapper
163 lines of code
performance
tagger.jensenlab.org/BeCalm
bottlenecks
network latency
text retrieval
Acknowledgments Evangelos Pafilis Sune Pletscher- Frankild Damian Szklarczyk Michael Kuhn

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