extr_comptox: Download and Extract Data from CompTox Chemistry Dashboard

In extractox: Extract Tox Info from Various Databases

Download and Extract Data from CompTox Chemistry Dashboard

Description

This function interacts with the CompTox Chemistry Dashboard to download and extract a wide range of chemical data based on user-defined search criteria. It allows for flexible input types and supports downloading various chemical properties, identifiers, and predictive data. It was inspired by the ECOTOXr::websearch_comptox function.

Usage

extr_comptox(
  ids,
  download_items = c("CASRN", "INCHIKEY", "IUPAC_NAME", "SMILES", "INCHI_STRING",
    "MS_READY_SMILES", "QSAR_READY_SMILES", "MOLECULAR_FORMULA", "AVERAGE_MASS",
    "MONOISOTOPIC_MASS", "QC_LEVEL", "SAFETY_DATA", "EXPOCAST", "DATA_SOURCES",
    "TOXVAL_DATA", "NUMBER_OF_PUBMED_ARTICLES", "PUBCHEM_DATA_SOURCES", "CPDAT_COUNT",
    "IRIS_LINK", "PPRTV_LINK", "WIKIPEDIA_ARTICLE", "QC_NOTES", "ABSTRACT_SHIFTER",
    "TOXPRINT_FINGERPRINT", "ACTOR_REPORT", "SYNONYM_IDENTIFIER", "RELATED_RELATIONSHIP",
    "ASSOCIATED_TOXCAST_ASSAYS", "TOXVAL_DETAILS", 
     "CHEMICAL_PROPERTIES_DETAILS",
    "BIOCONCENTRATION_FACTOR_TEST_PRED", "BOILING_POINT_DEGC_TEST_PRED",
    "48HR_DAPHNIA_LC50_MOL/L_TEST_PRED", "DENSITY_G/CM^3_TEST_PRED", "DEVTOX_TEST_PRED",
    "96HR_FATHEAD_MINNOW_MOL/L_TEST_PRED", "FLASH_POINT_DEGC_TEST_PRED",
    "MELTING_POINT_DEGC_TEST_PRED", "AMES_MUTAGENICITY_TEST_PRED",
    "ORAL_RAT_LD50_MOL/KG_TEST_PRED", "SURFACE_TENSION_DYN/CM_TEST_PRED",
    "THERMAL_CONDUCTIVITY_MW/(M*K)_TEST_PRED",
    "TETRAHYMENA_PYRIFORMIS_IGC50_MOL/L_TEST_PRED", "VISCOSITY_CP_CP_TEST_PRED", 
    
    "VAPOR_PRESSURE_MMHG_TEST_PRED", "WATER_SOLUBILITY_MOL/L_TEST_PRED",
    "ATMOSPHERIC_HYDROXYLATION_RATE_(AOH)_CM3/MOLECULE*SEC_OPERA_PRED",
    "BIOCONCENTRATION_FACTOR_OPERA_PRED",
    "BIODEGRADATION_HALF_LIFE_DAYS_DAYS_OPERA_PRED", "BOILING_POINT_DEGC_OPERA_PRED",
    "HENRYS_LAW_ATM-M3/MOLE_OPERA_PRED", "OPERA_KM_DAYS_OPERA_PRED",
    "OCTANOL_AIR_PARTITION_COEFF_LOGKOA_OPERA_PRED",
    "SOIL_ADSORPTION_COEFFICIENT_KOC_L/KG_OPERA_PRED",
    "OCTANOL_WATER_PARTITION_LOGP_OPERA_PRED", "MELTING_POINT_DEGC_OPERA_PRED", 
    
    "OPERA_PKAA_OPERA_PRED", "OPERA_PKAB_OPERA_PRED", "VAPOR_PRESSURE_MMHG_OPERA_PRED",
    "WATER_SOLUBILITY_MOL/L_OPERA_PRED",
    "EXPOCAST_MEDIAN_EXPOSURE_PREDICTION_MG/KG-BW/DAY", "NHANES",
    "TOXCAST_NUMBER_OF_ASSAYS/TOTAL", "TOXCAST_PERCENT_ACTIVE"),
  mass_error = 0,
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)

Arguments

ids	A character vector containing the items to be searched within the CompTox Chemistry Dashboard. These can be chemical names, CAS Registry Numbers (CASRN), InChIKeys, or DSSTox substance identifiers (DTXSID).
download_items	A character vector of items to be downloaded. This includes a comprehensive set of chemical properties, identifiers, predictive data, and other relevant information. By Default, it download all the info CASRN The Chemical Abstracts Service Registry Number, a unique numerical identifier for chemical substances. INCHIKEY The hashed version of the full International Chemical Identifier (InChI) string. IUPAC_NAME The International Union of Pure and Applied Chemistry (IUPAC) name of the chemical. SMILES The Simplified Molecular Input Line Entry System (SMILES) representation of the chemical structure. INCHI_STRING The full International Chemical Identifier (InChI) string. MS_READY_SMILES The SMILES representation of the chemical structure, prepared for mass spectrometry analysis. QSAR_READY_SMILES The SMILES representation of the chemical structure, prepared for quantitative structure-activity relationship (QSAR) modeling. MOLECULAR_FORMULA The chemical formula representing the number and type of atoms in a molecule. AVERAGE_MASS The average mass of the molecule, calculated based on the isotopic distribution of the elements. MONOISOTOPIC_MASS The mass of the molecule calculated using the most abundant isotope of each element. QC_LEVEL The quality control level of the data. SAFETY_DATA Safety information related to the chemical. EXPOCAST Exposure predictions from the EPA's ExpoCast program. DATA_SOURCES Sources of the data provided. TOXVAL_DATA Toxicological values related to the chemical. NUMBER_OF_PUBMED_ARTICLES The number of articles related to the chemical in PubMed. PUBCHEM_DATA_SOURCES Sources of data from PubChem. CPDAT_COUNT The number of entries in the Chemical and Product Categories Database (CPDat). IRIS_LINK Link to the EPA's Integrated Risk Information System (IRIS) entry for the chemical. PPRTV_LINK Link to the EPA's Provisional Peer-Reviewed Toxicity Values (PPRTV) entry for the chemical. WIKIPEDIA_ARTICLE Link to the Wikipedia article for the chemical. QC_NOTES Notes related to the quality control of the data. ABSTRACT_SHIFTER Information related to the abstract shifter. TOXPRINT_FINGERPRINT The ToxPrint chemoinformatics fingerprint of the chemical. ACTOR_REPORT The Aggregated Computational Toxicology Resource (ACTOR) report for the chemical. SYNONYM_IDENTIFIER Identifiers for synonyms of the chemical. RELATED_RELATIONSHIP Information on related chemicals. ASSOCIATED_TOXCAST_ASSAYS Assays associated with the chemical in the ToxCast database. TOXVAL_DETAILS Details of toxicological values. CHEMICAL_PROPERTIES_DETAILS Details of the chemical properties. BIOCONCENTRATION_FACTOR_TEST_PRED Predicted bioconcentration factor from tests. BOILING_POINT_DEGC_TEST_PRED Predicted boiling point in degrees Celsius from tests. 48HR_DAPHNIA_LC50_MOL/L_TEST_PRED Predicted 48-hour LC50 for Daphnia in mol/L from tests. DENSITY_G/CM^3_TEST_PRED Predicted density in g/cm³ from tests. DEVTOX_TEST_PRED Predicted developmental toxicity from tests. 96HR_FATHEAD_MINNOW_MOL/L_TEST_PRED Predicted 96-hour LC50 for fathead minnow in mol/L from tests. FLASH_POINT_DEGC_TEST_PRED Predicted flash point in degrees Celsius from tests. MELTING_POINT_DEGC_TEST_PRED Predicted melting point in degrees Celsius from tests. AMES_MUTAGENICITY_TEST_PRED Predicted Ames mutagenicity from tests. ORAL_RAT_LD50_MOL/KG_TEST_PRED Predicted oral LD50 for rats in mol/kg from tests. SURFACE_TENSION_DYN/CM_TEST_PRED Predicted surface tension in dyn/cm from tests. THERMAL_CONDUCTIVITY_MW_M×K_TEST_PRED Predicted thermal conductivity in mW/m×K from tests. TETRAHYMENA_PYRIFORMIS_IGC50_MOL/L_TEST_PRED Predicted IGC50 for Tetrahymena pyriformis in mol/L from tests. VISCOSITY_CP_CP_TEST_PRED Predicted viscosity in cP from tests. VAPOR_PRESSURE_MMHG_TEST_PRED Predicted vapor pressure in mmHg from tests. WATER_SOLUBILITY_MOL/L_TEST_PRED Predicted water solubility in mol/L from tests. ATMOSPHERIC_HYDROXYLATION_RATE_\(AOH\)_CM3/MOLECULE\*SEC_OPERA_PRED Predicted atmospheric hydroxylation rate in cm³/molecule\*sec from OPERA. BIOCONCENTRATION_FACTOR_OPERA_PRED Predicted bioconcentration factor from OPERA. BIODEGRADATION_HALF_LIFE_DAYS_DAYS_OPERA_PRED Predicted biodegradation half-life in days from OPERA. BOILING_POINT_DEGC_OPERA_PRED Predicted boiling point in degrees Celsius from OPERA. HENRYS_LAW_ATM-M3/MOLE_OPERA_PRED Predicted Henry's law constant in atm-m³/mole from OPERA. OPERA_KM_DAYS_OPERA_PRED Predicted Km in days from OPERA. OCTANOL_AIR_PARTITION_COEFF_LOGKOA_OPERA_PRED Predicted octanol-air partition coefficient (log Koa) from OPERA. SOIL_ADSORPTION_COEFFICIENT_KOC_L/KG_OPERA_PRED Predicted soil adsorption coefficient (Koc) in L/kg from OPERA. OCTANOL_WATER_PARTITION_LOGP_OPERA_PRED Predicted octanol-water partition coefficient (log P) from OPERA. MELTING_POINT_DEGC_OPERA_PRED Predicted melting point in degrees Celsius from OPERA. OPERA_PKAA_OPERA_PRED Predicted pKa (acidic) from OPERA. OPERA_PKAB_OPERA_PRED Predicted pKa (basic) from OPERA. VAPOR_PRESSURE_MMHG_OPERA_PRED Predicted vapor pressure in mmHg from OPERA. WATER_SOLUBILITY_MOL/L_OPERA_PRED Predicted water solubility in mol/L from OPERA. EXPOCAST_MEDIAN_EXPOSURE_PREDICTION_MG/KG-BW/DAY Predicted median exposure from ExpoCast in mg/kg-bw/day. NHANES National Health and Nutrition Examination Survey data. TOXCAST_NUMBER_OF_ASSAYS/TOTAL Number of assays in ToxCast. TOXCAST_PERCENT_ACTIVE Percentage of active assays in ToxCast.
mass_error	Numeric value indicating the mass error tolerance for searches involving mass data. Default is 0.
verify_ssl	Logical value indicating whether SSL certificates should be verified. Default is FALSE. Note that this argument is not used on linux OS.
verbose	A logical value indicating whether to print detailed messages. Default is TRUE.
...	Additional arguments passed to httr2::req_options().

Details

Please note that this function, which pulls data from EPA servers, may encounter issues on some Linux systems. This is because those servers do not accept secure legacy renegotiation. On Linux systems, the current function depends on curl and OpenSSL, which have known problems with unsafe legacy renegotiation in newer versions. One workaround is to downgrade to curl v7.78.0 and OpenSSL v1.1.1. However, please be aware that using these older versions might introduce potential security vulnerabilities. Refer to this gist for instructions on how to downgrade curl and OpenSSL on Ubuntu.

Value

A cleaned data frame containing the requested data from CompTox.

See Also

CompTox Chemicals Dashboard Resource Hub

Examples

# Example usage of the function:
extr_comptox(ids = c("Aspirin", "50-00-0"))

extractox documentation built on April 4, 2025, 2:30 a.m.