BioRelEx 1.0: Biological Relation Extraction Benchmark

AbstractAutomatic extraction of relations and interactions between biological entities from scientific literature remains an extremely challenging problem in biomedical information extraction and natural language processing in general. One of the reasons for slow progress is the relative scarcity of standardized and publicly available benchmarks. In this paper we introduce BioRelEx, a new dataset of fully annotated sentences from biomedical literature that capture binding interactions between proteins and/or biomolecules. To foster reproducible research on the interaction extraction task, we define a precise and transparent evaluation process, tools for error analysis and significance tests. Finally, we conduct extensive experiments to evaluate several baselines, including SciIE, a recently introduced neural multi-task architecture that has demonstrated state-of-the-art performance on several tasks.