get_2023pfasinfo: Retrieve chemical information on 2023 EPA PFAS Chemicals

In httk: High-Throughput Toxicokinetics

Retrieve chemical information on 2023 EPA PFAS Chemicals

Description

This function is a wrapper for get_cheminfo that only lists chemicals from the Smeltz, Kreutz, and Crizer data sets collected on PFAS between 2019 and 2022. Plasma protein binding (fraction unbound) data were collected using ultracentrifugation (UC) instead of rapid equilibrium dialysis. Intrsinsic hepatic clearance (Clint) data were collected with substrate depletion (over time) assays.

Usage

get_2023pfasinfo(
  info = "CAS",
  species = "Human",
  fup.lod.default = 0.005,
  model = "3compartmentss",
  default.to.human = FALSE,
  median.only = FALSE,
  fup.ci.cutoff = FALSE,
  clint.pvalue.threshold = 0.05,
  suppress.messages = FALSE
)

Arguments

info	A single character vector (or collection of character vectors) from "Compound", "CAS", "DTXSID, "logP", "pKa_Donor"," pKa_Accept", "MW", "Clint", "Clint.pValue", "Funbound.plasma","Structure_Formula", or "Substance_Type". info="all" gives all information for the model and species.
species	Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
fup.lod.default	Default value used for fraction of unbound plasma for chemicals where measured value was below the limit of detection. Default value is 0.0005.
model	Model used in calculation, 'pbtk' for the multiple compartment model, '1compartment' for the one compartment model, '3compartment' for three compartment model, '3compartmentss' for the three compartment model without partition coefficients, or 'schmitt' for chemicals with logP and fraction unbound (used in predict_partitioning_schmitt).
default.to.human	Substitutes missing values with human values if true.
median.only	Use median values only for fup and clint. Default is FALSE.
fup.ci.cutoff	Cutoff for the level of uncertainty in fup estimates. This value should be between (0,1). Default is 'NULL' specifying no filtering.
clint.pvalue.threshold	Hepatic clearance for chemicals where the in vitro clearance assay result has a p-values greater than the threshold are set to zero.
suppress.messages	Whether or not the output messages are suppressed.

Details

Note that in some cases the Funbound.plasma and the intrinsic clearance are provided as a series of numbers separated by commas. These values are the result of Bayesian analysis and characterize a distribution: the first value is the median of the distribution, while the second and third values are the lower and upper 95th percentile (that is qunatile 2.5 and 97.5) respectively. For intrinsic clearance a fourth value indicating a p-value for a decrease is provided. Typically 4000 samples were used for the Bayesian analusis, such that a p-value of "0" is equivale to "<0.00025". See Wambaugh et al. (2019) for more details. If argument meadian.only == TRUE then only the median is reported for parameters with Bayesian analysis distributions. If the 95 credible interval is larger than fup.ci.cutoff (defaults to NULL) then the Fup is treated as too uncertain and the value NA is given.

Value

vector/data.table

Table (if info has multiple entries) or vector containing a column for each valid entry specified in the argument "info" and a row for each chemical with sufficient data for the model specified by argument "model": Column Description units Compound The preferred name of the chemical compound none CAS The preferred Chemical Abstracts Service Registry Number none DTXSID DSSTox Structure ID (https://comptox.epa.gov/dashboard) none logP The log10 octanol:water partition coefficient log10 unitless ratio MW The chemical compound molecular weight g/mol pKa_Accept The hydrogen acceptor equilibria concentrations logarithm pKa_Donor The hydrogen donor equilibria concentrations logarithm [SPECIES].Clint (Primary hepatocyte suspension) intrinsic hepatic clearance uL/min/10^6 hepatocytes [SPECIES].Clint.pValue Probability that there is no clearance observed. none [SPECIES].Funbound.plasma Chemical fraction unbound in presence of plasma proteins unitless fraction [SPECIES].Rblood2plasma Chemical concentration blood to plasma ratio unitless ratio

Author(s)

John Wambaugh

Examples

PFASCssTable <- NULL
for (this.id in get_2023pfasinfo(info="dtxsid"))
{
  PFASCssTable <- rbind(PFASCssTable, data.frame(
    DTXSID = this.id,
    Css = try(calc_analytic_css(dtxsid=this.id, 
                                  model="sumclearancespfas",
                                  suppress.messages=TRUE
   ))))
}

httk documentation built on Aug. 29, 2025, 5:16 p.m.