Coreference resolution improves extraction of Biological Expression Language statements from texts

Miji Choi, Haibin Liu, William Baumgartner, Justin Zobel, Karin Verspoor
2016 Database: The Journal of Biological Databases and Curation  
We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreference resolution, biological event extraction and a previously formally untested strategy for BEL statement generation. Although addressing the BEL track (Track 4) at BioCreative V (2015), we also investigate how incorporating coreference resolution
more » ... ight impact event extraction in the biomedical domain. In this paper, we report that our system achieved the best performance of 20.2 and 35.2 in F-score for the full BEL statement level on both stage 1, and stage 2 using provided gold standard entities, respectively. We also report that our results evaluated on the training dataset show benefit from integrating coreference resolution with event extraction.
doi:10.1093/database/baw076 pmid:27374122 pmcid:PMC4930833 fatcat:7otkwc3stvcvhcb477zqtzg7ly