get_physchem_param

This function retrieves physico-chemical properties ("param") for the 
chemical specified by chem.name or chem.cas from the table
<code>chem.physical_and_invitro.data</code>. This 
function is distinguished from <code>get_invitroPK_param</code> in that
there are no species-specific values. Physically meaningful values for 
ionization equilibria are NA/none (that is, no ionization), a single value, 
or a series of values separated by commas. If logMA (log10 membrane affinity) 
is NA, we use calc_ma() to predict it later on in the model parameterization 
functions.

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_physchem_param function

<dl><dt>param</dt>
<dd>The desired parameters, a vector or single value.</dd>
<dt>chem.name</dt>
<dd>The chemical names that you want parameters for, a vector or single value</dd>
<dt>chem.cas</dt>
<dd>The chemical CAS numbers that you want parameters for, a vector or single value</dd>
<dt>dtxsid</dt>
<dd>EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard)
the chemical must be identified by either CAS, name, or DTXSIDs</dd></dl>

Arguments

Author

Get physico-chemical parameters from chem.physical_and_invitro.data table — get_physchem_param

<dl>

<dt>param</dt>
<dd>The desired parameters, a vector or single value.</dd>


<dt>chem.name</dt>
<dd>The chemical names that you want parameters for, a vector or single value</dd>


<dt>chem.cas</dt>
<dd>The chemical CAS numbers that you want parameters for, a vector or single value</dd>


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

</dl>

Get physico-chemical parameters from chem.physical_and_invitro.data table

Parameter	Description	Units
MW	Molecular weight	g/mole
pKa_Donor	Hydrogen donor ionization equilibria (acidic pKa)	pH
pKa_Accept	Hyrdogen acceptor ionization equilibria (basic pKa	pH
logMA	log10 Membrane Affinity	unitless
logP	log10 Octanol:Water Partition Coefficient (hydrophobicity)	unitless
logPwa	log10 Water:Air Partition Coefficient	unitless
logHenry	log10 Henry's Law Constant	atm-m3/mole
logWSol	log10 Water Solubility	moles/L: Water solubility at 25C
MP	Melting point	deg C

get_physchem_param: Get physico-chemical parameters from chem.physical_and_invitro.data table

Description

Usage

Value

Arguments

Author

Details

See Also

Examples