Mining, refining, and QSAR analysing the nanoinformatics in EPA NaKnowBase

Abstract

Concerns about the safety of manufacturing and using engineered nanomaterials (ENMs) have been increasing as the technology continues to expand. Efforts have been underway to investigate the potentially harmful effects of ENMs without carrying out the challenging empirical studies. To make such investigations possible, the US EPA Office of Research and Development (ORD) developed the nanomaterial database NaKnowBase (NKB) containing the detail of hundreds of assays conducted and published by ORD scientists experimentally investigating the environmental health and safety effects of ENMs (nanoEHS). This article describes specifics of the effort to mine, refine, and analyse the NKB. Here we use a quantitative structure activity relationship (QSAR) analysis, using a random forest of decision trees to predict the in vitro cell viability effects that occur upon exposure to ENMs that are similar in composition and structure and implement a set of laboratory conditions. These predictions are confirmed using the Jaqpot cloud platform developed by the National Technical University of Athens, Greece (NTUA) where nanoEHS effects are investigated with scientists working together globally.