Improvements to ToxCast Make Screening Assay Data for Thousands of Chemicals Easier to Interpret
Published March 10, 2025
EPA needs rapid and efficient methods to prioritize, evaluate, and regulate thousands of chemicals. However, generating traditional animal-based hazard data for all chemicals and chemical mixtures takes significant time and money. New approach methods (NAMs), such as EPA’s ToxCast assays, allow researchers to understand chemical hazards without whole animals, saving time and money in the research process.
EPA's Toxicity Forecaster (ToxCast) program provides in vitro medium- and high-throughput screening assay data to the public. In vitro assays are experiments that use components of an organism, like cells or proteins, to measure some response of a chemical at different concentrations. Assays may use a variety of technologies to evaluate the effects of chemical exposure at diverse biological targets such as cell or tissue cultures. ToxCast data covers almost 10,000 substances and is aggregated from 20 different assay sources, including the Toxicology in the 21st Century federal agency collaboration (TOX21) program.
ToxCast provides a standard for consistent and reproducible data processing for diverse, targeted bioactivity assay data with readily available documentation and transparent software development. This enables effective sharing and use of NAM data in various toxicology applications. ToxCast encompasses data processing software (tcpl, along with its dependency tcplfit2 and ctxR), a database of NAM information (known as invitrodb), and efforts to curate and make these data informative.
The most recent ToxCast database and software updates were released in September 2024, including invitrodb v4.2, tcpl v3.2, and tcplfit2 v0.1.7. The database release package includes:
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a MySQL database;
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release notes comparing version changes;
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summary files of data provided for convenience;
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assay descriptions to support interpretation; and
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concentration-response plots.
EPA also released updated versions of ToxCast Pipeline (tcpl, tcplfit2) and Computational Toxicology and Exposure (ctxR) open-source R packages. An R package is a collection of code, data, and documentation based on the R statistical programming language. The tcpl R package is used to process, model, visualize, and populate the linked MySQL database, invitrodb. tcpl also relies on tcplfit2, a curve-fitting utility for modeling the concentration-response data, and ctxR, a client package for interacting with the CTX Application Programming Interfaces (CTX APIs).
ToxCast bioactivity data can support chemical evaluations, user interfaces such as the CompTox Chemicals Dashboard, and research applications inside and outside of EPA. This update represents the second public ToxCast release following major software and database updates.
“With each update, we iteratively improve this resource to better support data interpretation and innovate with the science,” remarked Madison Feshuk, an EPA biologist and ToxCast curation lead. “This work is important if we want to confidently predict chemical toxicity without additional animal testing.”
As ToxCast improves, it continues to be a great resource that can help save time and money in the research process. For more information on ToxCast, visit the ToxCast webpage.