Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged. Results: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and dataanalysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various textmining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles. © The Author(s) 2010. Published by Oxford University Press.