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Area of Science:

  • Toxicology and Cheminformatics
  • Computational Biology and Bioinformatics
  • Environmental Health Sciences

Background:

  • The US Environmental Protection Agency Toxicity Forecaster (ToxCast) program generates extensive in vitro screening data for chemical hazard assessment.
  • The ToxCast data pipeline (tcpl) R package and invitrodb MySQL database manage and analyze this high-throughput screening data.
  • Existing curve-fitting models in tcpl were limited for comprehensive toxicological profiling.

Purpose of the Study:

  • To describe major updates to the tcpl R package and invitrodb database.
  • To incorporate a broader range of curve-fitting models for enhanced analysis of ToxCast data.
  • To improve the consistency, reproducibility, and utility of in vitro toxicology data.

Main Methods:

  • Expanded tcpl curve-fitting capabilities to include Polynomial, Power, and Exponential models, leveraging the tcplfit2 R package.
  • Modified invitrodb (beta version v4.0) to support new modeling parameters and updated model selection logic.
  • Implemented continuous hit calling logic and removed redundant endpoints through bidirectional fitting.

Main Results:

  • The updated tcpl and invitrodb (v4.0) accommodate a wider array of curve-fitting models.
  • Hit call and potency estimates remained largely consistent between invitrodb versions 3.5 and 4.0.
  • The enhancements facilitate standardized, reproducible curve-fitting and data management for in vitro toxicology data.

Conclusions:

  • Tcpl and invitrodb provide a robust standard for managing and analyzing diverse in vitro assay data.
  • These updates enhance data comparability across different tiers within the US Environmental Protection Agency CompTox Blueprint.
  • The improved software and database support broader applications of ToxCast data in toxicology and chemical risk assessment.