OGER++: hybrid multi-type entity recognition

Lenz Furrer, Anna Jancso, Nicola Colic, Fabio Rinaldi
2019 Journal of Cheminformatics  
We present a text-mining tool for recognizing biomedical entities in scientific literature. OGER++ is a hybrid system for named entity recognition and concept recognition (linking), which combines a dictionary-based annotator with a corpus-based disambiguation component. The annotator uses an efficient look-up strategy combined with a normalization method for matching spelling variants. The disambiguation classifier is implemented as a feed-forward neural network which acts as a postfilter to
more » ... e previous step. We evaluated the system in terms of processing speed and annotation quality. In the speed benchmarks, the OGER++ web service processes 9.7 abstracts or 0.9 full-text documents per second. On the CRAFT corpus, we achieved 71.4% and 56.7% F1 for named entity recognition and concept recognition, respectively. Combining knowledge-based and data-driven components allows creating a system with competitive performance in biomedical text mining.
doi:10.1186/s13321-018-0326-3 pmid:30666476 pmcid:PMC6689863 fatcat:mwhlaw5aqrhphbda7ze3dx6f5e