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Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System
Citation:
JUDSON, R. S., M. T. MARTIN, P. P. EGEGHY, S. GANGWAL, D. M. REIF, P. KOTHIYA, M. A. WOLF, T. CATHEY, T. R. TRANSUE, D. SMITH, J. VAIL, A. FRAME, S. MOSHER, E. A. COHEN-HUBAL, AND A. M. RICHARD. Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System. International Journal of Molecular Sciences. MDPI, Basel, Switzerland, 13(2):1805-1831, (2012).
Impact/Purpose:
Any one database (or data warehouse) cannot hope to hold all relevant chemical or toxicology data, and different groups will design their database and user interfaces to meet variant use cases. Coordinating these databases or other sources of information will enhance all users’ searches. However, it is important in a world of limited resources to make sure that all of these public data resources make as much use of one another as possible. All these efforts contribute to the goal of ensuring maximal transparency and ease of public access to important data on the large number of chemicals in the environment.
Description:
Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases.
