Text Mining Tools for Studying Kinase-Substrate Networks and Protein Interaction Networks of Phosphorylated Proteins

Protein phosphorylation is a central regulatory mechanism in signal transduction involved in most biological processes. Kinases are responsible for protein phosphorylation, which may lead to activation or repression of its activity, alternative subcellular location, and interaction with different binding partners. Extracting this type of information from scientific literature is critical for connecting phosphorylated proteins with kinases and interaction partners, along with their functional outcomes, for knowledge discovery from phosphorylation protein networks. We have developed two text mining tools that provide complementary information about protein phosphorylation: RLIMS-P extracts information about kinase, substrate and phosphorylation sites; and eFIP text mining system combines several natural language processing techniques to find relevant abstracts mentioning phosphorylation of a given protein together with indications of protein-protein interactions (PPIs) and potential evidences for impact of phosphorylation on the PPIs. In this workshop we will demonstrate how to utilize these publicly available tools to collect information about kinase-substrate networks and protein interaction networks of phosphorylated proteins through case studies.