Introduction
The Toxicological Prioritization Index (ToxPi) is a framework used to integrate diverse data from multiple sources to create a visual and numerical ranking of chemicals or other entities. The ToxPi framework is particularly useful in toxicology for assessing potential risks based on multiple lines of evidence, but its flexible design allows it to be applied to other complex datasets, including geospatial and public health data.
Software
ToxPi is available in the following software distributions that are under active development.
toxpiR
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GitHub for toxpiR package (includes branches under active development with new features): toxpiR GitHub
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CRAN version of toxpiR package (stable release): toxpiR on CRAN
ToxPi Java GUI
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Direct download of the Stand-alone Java application (GUI) from toxpi.org: toxpi_v2.3.zip
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Direct download the GUI User Manual (PDF) from toxpi.org/Manual: ToxPi User Manual.pdf
ToxPi*GIS
- Toolkit for integrating ToxPi models with GIS mapping applications: https://www.nature.com/articles/s41370-022-00433-w
Publications
The major methodological publications are listed in chronological order in Methods. The section Applications & Citations links out to peer-reviewed journal publications, as well as applications where ToxPi has featured in official documents from the International Agency for Research on Cancer (IARC), the National Academy of Sciences (NAS), the U.S. Environmental Protection Agency (US EPA), and other translational science bodies.
Methods
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Fleming JF, House JS, Chappel JR, Motsinger-Reif AA, Reif DM. Guided optimization of ToxPi model weights using a Semi-Automated approach. Comput Toxicol. 2024 Mar;29:100294. https://pmc.ncbi.nlm.nih.gov/articles/PMC11175362/
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Fleming J, Marvel SW, Supak S, Motsinger-Reif AA, Reif DM. ToxPi*GIS Toolkit: creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS. J Expo Sci Environ Epidemiol. 2022 Apr 26:1–8. https://www.nature.com/articles/s41370-022-00433-w
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Marvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics. 2018. 19(1):80. https://doi.org/10.1186/s12859-018-2089-2
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Filer DL, Patisaul HB, Schug T, Reif D, Thayer, K. Test driving ToxCast: endocrine profiling for 1858 chemicals included in phase II. Current Opinion in Pharmacology. 2014. 19:145-152. https://doi.org/10.1016/j.coph.2014.09.021 →Methodological advancement in score calculation used in all subsequent ToxPi implementations
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Reif DM, Martin MT, Tan SW, Houck KA, Judson RS, Richard AM, Knudsen TB, Dix DJ, Kavlock RF. Endocrine profiling and prioritization of environmental chemicals using ToxCast data. Environmental Health Perspectives. 2010. 118(12):1714-20. https://doi.org/10.1289/ehp.1002180