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Mining, refining, and QSAR analysing the nanoinformatics in EPA NaKnowBase
Citation:
Harten, P., H. Helgen, W. Melendez, B. Beach, W. Boyes, I. Sotiropoulos, P. Karatzas, H. Sarimveis, AND H. Mortensen. Mining, refining, and QSAR analysing the nanoinformatics in EPA NaKnowBase. Environmental Science: Nano. Royal Society of Chemistry, Cambridge, Uk, 11:2262-2274, (2024). https://doi.org/10.1039/D3EN00619K
Impact/Purpose:
This paper shows processing of the nanoinformatic data within NaKnowBase to build the Quantitative Structure Activity (QSAR) modeling tool nanoQSAR. The viability of cell cultures predictions are made by training a random forest of decision trees, and then using this trained forest to make predictions on new test data. The nanoQSAR tool has been made available for predictions at the Jaqpot website in collaboration with the National Technical University of Athens, Greece.
Description:
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.
