Motivation: Knowledge of drug-drug interactions (DDIs) is crucial for health-care professionals to avoid adverse effects when co-administering drugs to patients. As most newly discovered DDIs are made available through scientific publications, automatic DDI extraction is highly relevant. Results: We propose a novel feature-based approach to extract DDIs from text. Our approach consists of three steps. First, we apply text preprocessing to convert input sentences from a given dataset into structured representations. Second, we map each candidate DDI pair from that dataset into a suitable syntactic structure. Based on that, a novel set of features is used to generate feature vectors for these candidate DDI pairs. Third, the obtained feature vectors are used to train a support vector machine (SVM) classifier. When evaluated on two DDI extraction challenge test datasets from 2011 and 2013, our system achieves F-scores of 71.1% and 83.5%, respectively, outperforming any state-of-the-art DDI extraction system.

Additional Metadata
Persistent URL dx.doi.org/10.1093/bioinformatics/btu557, hdl.handle.net/1765/83802
Journal Bioinformatics
Citation
Bui, Q.C, Sloot, P.M.A, Van Mulligen, E.M, & Kors, J.A. (2014). A novel feature-based approach to extract drug-drug interactions from biomedical text. Bioinformatics, 30(23), 3365–3371. doi:10.1093/bioinformatics/btu557