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Extract 2.0: Text-mining-assisted interactive annotation

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Lars Juhl Jensen
Lars Juhl Jensen

Extract 2.0: Text-mining-assisted interactive annotation

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Lars Juhl Jensen @larsjuhljensen Extract 2.0 Text-mining-assisted interactive annotation
>10 km
too much to read
text mining
interactive annotation
bookmarklet
identify relevant sections
extract normalized entities
Pafilis et al., Database, 2016extract.hcmr.gr
dictionary
genes / proteins
chemical compounds
organisms
Gene Ontology terms
tissues
diseases
phenotypes
environments
not comprehensive
expansion rules
plural / adjective forms
abbreviated forms
curated blacklist
SDS
software
C++ engine
flexible matching
70–80% recall
80–90% precision
>1000 abstracts / second
inherently thread-safe
Python wrapper
web service
open source
evaluation
BioCreative V IAT
evaluated by curators
positive user feedback
Wang et al., Database, 2016
BioCreative V.5 TIPS
perfect uptime
minimal response time
Jensen, Proceedings of BioCreative V.5, 2017tagger.jensenlab.org/BeCalm
Acknowledgments Evangelos Pafilis Sune Pletscher-Frankild Damian Szklarczyk Michael Kuhn Christos Arvanitidis
Extract 2.0: Text-mining-assisted interactive annotation
Extract 2.0: Text-mining-assisted interactive annotation

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