get_caco2

This function checks for chemical-specific in vitro measurements of the 
Caco-2 membrane permeability 
in the <code>chem.physical_and_invitro.data</code> table. If no value is 
available argument <code>Caco2.Pab.default</code> is returned.
Anywhere that the values is reported by three numbers separated by a comma 
(this also happens for plasma protein binding) the three values are: median, 
lower 95 percent confidence intervals, upper 95 percent confidence interval. Unless you are 
doing monte carlo work it makes sense to ignore the second and third values.

Parameter

oral_bioavailability

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

get_caco2 function

<dl><dt>chem.cas</dt>
<dd>Chemical Abstract Services Registry Number (CAS-RN) -- the 
chemical must be identified by either CAS, name, or DTXISD</dd>
<dt>chem.name</dt>
<dd>Chemical name (spaces and capitalization ignored) -- the 
chemical must be identified by either CAS, name, or DTXISD</dd>
<dt>dtxsid</dt>
<dd>EPA's DSSTox Structure ID (<a href="https://comptox.epa.gov/dashboard">https://comptox.epa.gov/dashboard</a>)
-- the chemical must be identified by either CAS, name, or DTXSIDs</dd>
<dt>Caco2.Pab.default</dt>
<dd>sets the default value for Caco2.Pab if Caco2.Pab is 
unavailable.</dd>
<dt>suppress.messages</dt>
<dd>Whether or not the output message is suppressed.</dd></dl>

Arguments

Author

Retrieve in vitro measured Caco-2 membrane permeabilit — get_caco2

<dl>

<dt>chem.cas</dt>
<dd>Chemical Abstract Services Registry Number (CAS-RN) -- the 
chemical must be identified by either CAS, name, or DTXISD</dd>


<dt>chem.name</dt>
<dd>Chemical name (spaces and capitalization ignored) -- the 
chemical must be identified by either CAS, name, or DTXISD</dd>


<dt>dtxsid</dt>
<dd>EPA's DSSTox Structure ID (<a href='https://comptox.epa.gov/dashboard'>https://comptox.epa.gov/dashboard</a>)
-- the chemical must be identified by either CAS, name, or DTXSIDs</dd>


<dt>Caco2.Pab.default</dt>
<dd>sets the default value for Caco2.Pab if Caco2.Pab is 
unavailable.</dd>


<dt>suppress.messages</dt>
<dd>Whether or not the output message is suppressed.</dd>

</dl>

Retrieve in vitro measured Caco-2 membrane permeabilit

get_caco2: Retrieve in vitro measured Caco-2 membrane permeabilit

Description

Usage

Arguments

Author