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Software and database enhancements to ToxCast supporting continued integration and use of in vitro bioactivity screening data
Citation:
Feshuk, M., J. Brown, S. Davidson-Fritz, K. Carstens, A. Ko, C. Thunes, R. Judson, AND K. Friedman. Software and database enhancements to ToxCast supporting continued integration and use of in vitro bioactivity screening data. ASCCT, Silver Spring, MD, October 23 - 25, 2023. https://doi.org/10.23645/epacomptox.24347596
Impact/Purpose:
The ToxCast data pipeline (tcpl) is an open-source R package that stores, manages, curve-fits, and visualizes ToxCast data as well as populating the linked MySQL Database, InvitroDB. These Tcpl and InvitroDB enhancements will support the continued utility of ToxCast in vitro screening results as a resource for bioactivity data in myriad toxicology applications.
Description:
The US Environmental Protection Agency Toxicity Forecaster (ToxCast) program makes in vitro medium- and high-throughput screening assay data publicly available for prioritization and hazard characterization. The ToxCast data pipeline (tcpl) is an open-source R package that stores, manages, curve-fits, and visualizes ToxCast data as well as populating the linked MySQL database, invitrodb. Evolving data needs for next generation risk assessment necessitated software and database updates for consistent and reproducible curve-fitting and data management across screening efforts. Largely motivated by a desire to utilize a single curve-fitting approach as encoded by the R package tcplfit2, these changes promote comparability across multiple tiers of bioactivity data within the CompTox Blueprint, including not only targeted ToxCast assays (Tiers 2-3), but also with broad coverage, high content assays in Tier 1, such as transcriptomics or phenotypic profiling. Major updates to tcpl and invitrodb include inclusion of additional models, bidirectional curve-fitting, continuous hit calling, and modified annotation structure, as well as new fit categories and updated cautionary flagging based on observed curve-fitting behavior. Overall, these updates resulted in minimal changes in activity hit calls and potency estimates. ToxCast provides a standard for consistent and reproducible curve-fitting and data management for diverse, targeted in vitro assay data with readily available documentation, thus enabling the sharing and use of these data in myriad toxicology applications. Together, these updates to tcpl and invitrodb improve the utility of ToxCast data within an integrated NAM strategy and unified open-source software approach. This abstract does not necessarily reflect U.S. EPA policy.
URLs/Downloads:
DOI: Software and database enhancements to ToxCast supporting continued integration and use of in vitro bioactivity screening data
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