PPIExtractor: A protein-protein interaction Extractor for biomédical literature

Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. In this paper, we present a PPI extraction system, termed PPIExtractor, which automatically extracts PPIs from biomedical text and visualizes them. Given a Medline record dataset, PPIExtractor first applies Feature Coupling Generalization (FCG) to tag protein names, next uses the extended semantic similarity-based method to normalize them, then combines feature-based, convolution tree and graph kernels to extract PPIs, and finally visualizes the PPI network. Experimental evaluations show that PPIExtractor can achieve state-of-the-art performance on a DIP subset with respect to comparable evaluations. PPIExtractor is freely available for academic purposes at: http://202.118.75.18:8080/PPIExtractor/.