Mining, refining, and QSAR analysing the nanoinformatics in EPA NaKnowBase.
Paul Harten, Henry Helgen, Wilson Melendez, Bradley Beach, William K Boyes, Iason Sotiropoulos, Pantelis Karatzas, Haralambos Sarimveis, Holly M Mortensen
Author Information
Paul Harten: Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, AWBERC MS 483, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA. ORCID
Henry Helgen: General Dynamics Information Technology, 3150 Fairview Park Drive, Falls Church, VA 22042, USA.
Wilson Melendez: General Dynamics Information Technology, 6201 Congdon Boulevard, Duluth, MN 55804, USA.
Bradley Beach: Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA.
William K Boyes: Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA.
Iason Sotiropoulos: School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechneiou St., 15780, Athens, Greece.
Pantelis Karatzas: School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechneiou St., 15780, Athens, Greece.
Haralambos Sarimveis: School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechneiou St., 15780, Athens, Greece. ORCID
Holly M Mortensen: Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA. ORCID
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 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.
