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InVitroDB Version 4.1
Citation:
Brown, J., M. Feshuk, AND K. Friedman. InVitroDB Version 4.1. U.S. Environmental Protection Agency, Washington, DC, 2023. https://doi.org/10.23645/epacomptox.6062623.v11
Impact/Purpose:
N/A
Description:
Invitrodb version 4.1 represents the fi rst full release of the ToxCast database in a new schema designed toaccommodate the R package dependency, tcplFit2, which is used in curve-fi tti ng and hit-calling of multi -concentrati onresponse data. This invitrodb schema was beta-tested with our research release of invitrodb v4.0 to accompany themanuscript, “The ToxCast Pipeline: Updates to Curve-Fitti ng Approaches and Database Structure” and release of tcplv3.0.1. Invitrodb v4.1 demonstrates a reduced number of total assay endpoints from invitrodb v3.5. As tcplfi t2 allowsfor bidirecti onal fi tti ng, we needed to make a major revision to how ToxCast data stored. Data are now curve-fi t bidirecti onally (or in a single directi on if appropriate), and as such, “up” and “dn” endpoints are no longerneeded to capture bidirecti onal eff ects. Overall this results in the greatest change between invitrodb version3.5 and the invitrodb version 4.1: the number of assay endpoints is actually decreased, refl ecti ng a reducti on inredundant “up” and “dn” curve-fi tti ng (see “Assay Endpoint Review”). Invitrodb v4.1 reintroduces level 6 “cauti on fl ags” on curve-fi tti ng. These were re-developed post invitrodbv4.0, based on the curve behaviors observed in invitrodb v4.0 (see “Cauti on Flag Review”). Invitrodb v4.1 updates the cytotoxicity threshold calculati on. Another key change introduced in the currentversion of tcpl v3.0.2 is an update to the cytotoxicity threshold or “burst” esti mates that are calculated withtcpl::tcplCytoPt() (see “Cytotoxicity Threshold Review”). Minor changes in hitcall from invitrodb v4.0 (beta release) to invitrodb v4.1 are expected based on a bug fi x inlibrary(tcplfi t2) to consider the median response at each concentrati on rather than any response at eachconcentrati on with respect to the cutoff (see “Hitrates by assay source”). Recent eff orts in the US EPA Offi ce of Research and Development have yielded targeted assay data for per- andpolyfl uoroalkyl substances (PFAS). Sample quality control informati on from this recent eff ort are availablepublicly and can be linked directly by sample identi fi er (spid) or at the chemical level (DSSTox substanceidenti fi er), based on inference that other samples would behave like the sample evaluated (see “PFAS data andsample quality control”).
URLs/Downloads:
DOI: InVitroDB Version 4.1
https://clowder.edap-cluster.com/spaces/647f710ee4b08a6b394e426b