PPIExtractor: a protein interaction extraction and visualization system for biomedical literature

Protein-protein interactions (PPIs) play a key role in various aspects of the structural and functional organization of the cell. Knowledge about them unveils the molecular mechanisms of biological processes. However, the amount of biomedical literature regarding protein interactions is increasing rapidly and it is difficult for interaction database curators to detect and curate protein interaction information manually. 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 in text, 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.