honda2023.qspr

<p>Honda et al. (2023) describes the construction of a machine-learning 
quantitative structure-property relationship (QSPR )model for in vitro Caco-2 
membrane permeabilites. That model was used to make chemical-specific 
predictions provided in this table.</p>

datasets

Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments.   The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predictions for chemicals
where in vivo data do exist. The models are systems of ordinary
differential equations that are developed in MCSim and solved
using compiled (C-based) code for speed. A Monte Carlo sampler is
included for simulating human biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and propagating parameter uncertainty
(Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>).
Empirically calibrated methods are included for predicting
tissue:plasma partition coefficients and volume of distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for using IVIVE to
convert concentrations from high-throughput screening experiments
(for example, Tox21, ToxCast) to real-world exposures via reverse
dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

John Wambaugh

httk

High-Throughput Toxicokinetics

Sarah Davidson-Fritz

Robert Pearce

Caroline Ring

Greg Honda

Mark Sfeir

Matt Linakis

Dustin Kapraun

Nathan Pollesch

Miyuki Breen

Shannon Bell

Xiaoqing Chang

Todor Antonijevic

Jimena Davis

Elaina Kenyon

Katie Paul Friedman

Celia Schacht

Meredith Scherer

James Sluka

Noelle Sinski

Nisha Sipes

Barbara Wetmore

Lily Whipple

Woodrow Setzer

honda2023.qspr function

<p>An object of class <code>data.frame</code> with 14033 rows and 5 columns.</p>

Format

Predicted Caco-2 Apical-Basal Permeabilities — honda2023.qspr

Predicted Caco-2 Apical-Basal Permeabilities

Column Name	Description	Units
DTXSID	EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard)
Pab.Class.Pred	Predicted Pab rate of slow (1), moderate (2), or fast (3)
Pab.Pred.AD	Whether (1) or not (0) the chemical is anticipated to be withing the QSPR domain of applicability
CAS	Chemical Abstracts Service Registry Number
Pab.Quant.Pred	Median and 95-percent interval for values within the predicted class's training data moderate (2), or fast (3)	10^-6 cm/s

honda2023.qspr: Predicted Caco-2 Apical-Basal Permeabilities

Description

Usage

Arguments

Format

Details

References

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