Event extraction for systems biology by text mining the literature

Systems biology recognizes in particular the importance of interactions between biological components and the consequences of these interactions. Such interactions and their downstream effects are known as events. To computationally mine the literature for such events, text mining methods that can detect, extract and annotate them are required. This review summarizes the methods that are currently available, with a specific focus on protein–protein interactions and pathway or network reconstruction. The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states.