get_clint

This function retrieves the chemical- and species-specific intinsic
hepatic clearance (Clint,
inits of uL/min/million hepatocytes) 
from <code>chem.physical_and_invitro.data</code>. 
If that parameter is described by a distribution (that is, a median, 
lower-, upper-95th percentile and p-value separated by commas) this 
function splits those quantiles into separate values. Most 
Clint values have an
accompanying p-value indicating the probability that no decrease was 
observed. If the p-values exceeds a threhsold (default 0.05) the clearance is
set to zero (no clearance). Some values extracted from the literature do not
have a p-value.

Parameter

in-vitro

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_clint function

<dl><dt>chem.cas</dt>
<dd>Chemical Abstract Services Registry Number (CAS-RN) -- if
parameters is not specified then the chemical must be identified by either
CAS, name, or DTXISD</dd>
<dt>chem.name</dt>
<dd>Chemical name (spaces and capitalization ignored) -- if
parameters is not specified then 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>)
 -- if parameters is not specified then the chemical must be identified by 
either CAS, name, or DTXSIDs</dd>
<dt>species</dt>
<dd>Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or
default "Human").</dd>
<dt>default.to.human</dt>
<dd>Substitutes missing hepatic clearance with
human values if true.</dd>
<dt>force.human.clint</dt>
<dd>If a non-human species value (matching argument
species) is available, it is ignored and the human intrinsic clearance is 
used</dd>
<dt>suppress.messages</dt>
<dd>Whether or not the output message is suppressed.</dd>
<dt>clint.pvalue.threshold</dt>
<dd>Hepatic clearance for chemicals where the in
vitro clearance assay result has a p-values greater than the threshold are
set to zero.</dd></dl>

Arguments

Author

Retrieve and parse intrinsic hepatic clearance — get_clint

<dl>

<dt>chem.cas</dt>
<dd>Chemical Abstract Services Registry Number (CAS-RN) -- if
parameters is not specified then the chemical must be identified by either
CAS, name, or DTXISD</dd>


<dt>chem.name</dt>
<dd>Chemical name (spaces and capitalization ignored) -- if
parameters is not specified then 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>)
 -- if parameters is not specified then the chemical must be identified by 
either CAS, name, or DTXSIDs</dd>


<dt>species</dt>
<dd>Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or
default "Human").</dd>


<dt>default.to.human</dt>
<dd>Substitutes missing hepatic clearance with
human values if true.</dd>


<dt>force.human.clint</dt>
<dd>If a non-human species value (matching argument
species) is available, it is ignored and the human intrinsic clearance is 
used</dd>


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


<dt>clint.pvalue.threshold</dt>
<dd>Hepatic clearance for chemicals where the in
vitro clearance assay result has a p-values greater than the threshold are
set to zero.</dd>

</dl>

Retrieve and parse intrinsic hepatic clearance

get_clint: Retrieve and parse intrinsic hepatic clearance

Description

Usage

Value

Arguments

Author

See Also