Package 'extractox' reference manual

Title:	Extract Tox Info from Various Databases
Description:	Extract toxicological and chemical information from databases maintained by scientific agencies and resources, including the Comparative Toxicogenomics Database <https://ctdbase.org/>, the Integrated Chemical Environment <https://ice.ntp.niehs.nih.gov/>, the Integrated Risk Information System <https://cfpub.epa.gov/ncea/iris/>, the CompTox Chemicals Dashboard Resource Hub <https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard-resource-hub>, and PubChem <https://pubchem.ncbi.nlm.nih.gov/>.
Authors:	Claudio Zanettini [aut, cre, cph] , Lucio Queiroz [aut]
Maintainer:	Claudio Zanettini <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.9001
Built:	2024-12-19 03:37:45 UTC
Source:	https://github.com/c1au6i0/extractox

Retrieve CASRN for PubChem CIDs

Description

This function retrieves the CASRN for a given set of PubChem Compound Identifiers (CID). It queries PubChem through the webchem package and extracts the CASRN from the depositor-supplied synonyms.

Usage

extr_casrn_from_cid(pubchem_id, verbose = TRUE)
extr_casrn_from_cid(pubchem_id, verbose = TRUE)

Arguments

`pubchem_id`	A numeric vector of PubChem CIDs. These are unique identifiers for chemical compounds in the PubChem database.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A data frame containing the CID, CASRN, and IUPAC name of the compound. The returned data frame includes three columns:

CID: The PubChem Compound Identifier.
cas_rn: The corresponding CASRN of the compound.
IUPACName: The IUPAC name of the compound.

Examples


# Example with formaldehyde and aflatoxin
cids <- c(712, 14434) # CID for formaldehyde and aflatoxin B1
extr_casrn_from_cid(cids)

# Example with formaldehyde and aflatoxin
cids <- c(712, 14434) # CID for formaldehyde and aflatoxin B1
extr_casrn_from_cid(cids)

Query Chemical Information from IUPAC Names

Description

This function takes a vector of IUPAC names and queries the PubChem database (using the webchem package) to obtain the corresponding CASRN and CID for each compound. It reshapes the resulting data, ensuring that each compound has a unique row with the CID, CASRN, and additional chemical properties.

Usage

extr_chem_info(IUPAC_names, stop_on_warning = FALSE, verbose = TRUE)
extr_chem_info(IUPAC_names, stop_on_warning = FALSE, verbose = TRUE)

Arguments

`IUPAC_names`	A character vector of IUPAC names. These are standardized names of chemical compounds that will be used to search in the PubChem database.
`stop_on_warning`	Logical. If set to TRUE, the function will stop and throw an error if any substances are not found in PubChem. Defaults to FALSE, in which case a warning is issued.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A data frame with information on the queried compounds, including:

iupac_name: The IUPAC name of the compound.
cid: The PubChem Compound Identifier (CID).
isomeric_smiles: The SMILES string (Simplified Molecular Input Line Entry System).

Examples


# Example with formaldehyde and aflatoxin
extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))

# Example with formaldehyde and aflatoxin
extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))

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,
  ...
)
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()`. Note that this argument is not used on linux OS.

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.

Examples


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

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

Extract Data from the CTD API

Description

This function queries the Comparative Toxicogenomics Database API to retrieve data related to chemicals, diseases, genes, or other categories.

Usage

extr_ctd(
  input_terms,
  category = "chem",
  report_type = "genes_curated",
  input_term_search_type = "directAssociations",
  action_types = NULL,
  ontology = NULL,
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)
extr_ctd(
  input_terms,
  category = "chem",
  report_type = "genes_curated",
  input_term_search_type = "directAssociations",
  action_types = NULL,
  ontology = NULL,
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)

Arguments

`input_terms`	A character vector of input terms such as CAS numbers or IUPAC names.
`category`	A string specifying the category of data to query. Valid options are "all", "chem", "disease", "gene", "go", "pathway", "reference", and "taxon". Default is "chem".
`report_type`	A string specifying the type of report to return. Default is "genes_curated". Valid options include: "cgixns" Curated chemical-gene interactions. Requires at least one `action_types` parameter. "chems" All chemical associations. "chems_curated" Curated chemical associations. "chems_inferred" Inferred chemical associations. "genes" All gene associations. "genes_curated" Curated gene associations. "genes_inferred" Inferred gene associations. "diseases" All disease associations. "diseases_curated" Curated disease associations. "diseases_inferred" Inferred disease associations. "pathways_curated" Curated pathway associations. "pathways_inferred" Inferred pathway associations. "pathways_enriched" Enriched pathway associations. "phenotypes_curated" Curated phenotype associations. "phenotypes_inferred" Inferred phenotype associations. "go" All Gene Ontology (GO) associations. Requires at least one `ontology` parameter. "go_enriched" Enriched GO associations. Requires at least one `ontology` parameter.
`input_term_search_type`	A string specifying the search method to use. Options are "hierarchicalAssociations" or "directAssociations". Default is "directAssociations".
`action_types`	An optional character vector specifying one or more interaction types for filtering results. Default is "ANY". Other acceptable inputs are "abundance", "activity", "binding", "cotreatment", "expression", "folding", "localization", "metabolic processing"...See https://ctdbase.org/tools/batchQuery.go for a full list.
`ontology`	An optional character vector specifying one or more ontologies for filtering GO reports. Default NULL.
`verify_ssl`	Boolean to control of SSL should be verified or not.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.
`...`	Any other arguments to be supplied to `req_option` and thus to `libcurl`.

Value

A data frame containing the queried data in CSV format.

References

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, T. C., & Mattingly, C. J. (2019). The Comparative Toxicogenomics Database: update 2019. Nucleic acids research, 47(D1), D948–D954. doi:10.1093/nar/gky868

Examples


input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol")
dat <- extr_ctd(
  input_terms = input_terms,
  category = "chem",
  report_type = "genes_curated",
  input_term_search_type = "directAssociations",
  action_types = "ANY",
  ontology = c("go_bp", "go_cc")
)
str(dat)

# Get expresssion data
dat2 <- extr_ctd(
  input_terms = input_terms,
  report_type = "cgixns",
  category = "chem",
  action_types = "expression"
)

str(dat2)

input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol")
dat <- extr_ctd(
  input_terms = input_terms,
  category = "chem",
  report_type = "genes_curated",
  input_term_search_type = "directAssociations",
  action_types = "ANY",
  ontology = c("go_bp", "go_cc")
)
str(dat)

# Get expresssion data
dat2 <- extr_ctd(
  input_terms = input_terms,
  report_type = "cgixns",
  category = "chem",
  action_types = "expression"
)

str(dat2)

Extract Data from NTP ICE Database

Description

The extr_ice function sends a POST request to the ICE API to search for information based on specified chemical IDs and assays.

Usage

extr_ice(casrn, assays = NULL, verify_ssl = FALSE, verbose = TRUE, ...)
extr_ice(casrn, assays = NULL, verify_ssl = FALSE, verbose = TRUE, ...)

Arguments

`casrn`	A character vector specifying the CASRNs for the search.
`assays`	A character vector specifying the assays to include in the search. Default is NULL, meaning all assays are included. If you don't know the exact assay name, you can use the `extr_ice_assay_names()` function to search for assay names that match a pattern you're interested in.
`verify_ssl`	Boolean to control of SSL should be verified or not.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.
`...`	Any other arguments to be supplied to `req_option` and thus to `libcurl`.

Value

A data frame containing the extracted data from the ICE API.

Examples


extr_ice(c("50-00-0"))

extr_ice(c("50-00-0"))

Extract Assay Names from the ICE Database

Description

This function allows users to search for assay names in the ICE database using a regular expression. If no search pattern is provided (regex = NULL), it returns all available assay names.

Usage

extr_ice_assay_names(regex = NULL)
extr_ice_assay_names(regex = NULL)

Arguments

regex

A character string containing the regular expression to search for, or NULL to retrieve all assay names.

Value

A character vector of matching assay names.

Examples


extr_ice_assay_names("OPERA")
extr_ice_assay_names(NULL)
extr_ice_assay_names("Vivo")

extr_ice_assay_names("OPERA")
extr_ice_assay_names(NULL)
extr_ice_assay_names("Vivo")

Extract Data from EPA IRIS Database

Description

The extr_iris function sends a request to the EPA IRIS database to search for information based on a specified keywords and cancer types. It retrieves and parses the HTML content from the response. Note that if keywords is not provide all dataset are retrieved.

Usage

extr_iris(
  casrn = NULL,
  cancer_types = c("non_cancer", "cancer"),
  verbose = TRUE
)
extr_iris(
  casrn = NULL,
  cancer_types = c("non_cancer", "cancer"),
  verbose = TRUE
)

Arguments

`casrn`	A vector CASRN for the search.
`cancer_types`	A character vector specifying the types of cancer to include in the search. Must be either "non_cancer" or "cancer".
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A data frame containing the extracted data.

Examples


extr_iris(c("1332-21-4", "50-00-0"))

extr_iris(c("1332-21-4", "50-00-0"))

Retrieve WHO IARC Monograph Information

Description

This function retrieves information regarding Monographs from the World Health Organization (WHO) International Agency for Research on Cancer (IARC) based on CAS Registry Number or Name of the chemical.

Usage

extr_monograph(ids, search_type = "casrn", verbose = TRUE)
extr_monograph(ids, search_type = "casrn", verbose = TRUE)

Arguments

`ids`	A character vector of IDs to search for.
`search_type`	A character string specifying the type of search to perform. Valid options are "cas_rn" (CAS Registry Number) and "name" (name of the chemical). If `search_type` is "casrn", the function filters by the CAS Registry Number. If `search_type` is "name", the function performs a partial match search for the chemical name.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A data frame containing the relevant information from the WHO IARC, including Monograph volume, volume_publication_year, evaluation_year, and additional_information where the chemical was described.

Examples

{
  dat <- extr_monograph(search_type = "casrn", ids = c("105-74-8", "120-58-1"))
  str(dat)

  # Example usage for name search
  dat2 <- extr_monograph(search_type = "name", ids = c("Aloe", "Schistosoma", "Styrene"))
  str(dat2)
}
{
  dat <- extr_monograph(search_type = "casrn", ids = c("105-74-8", "120-58-1"))
  str(dat)

  # Example usage for name search
  dat2 <- extr_monograph(search_type = "name", ids = c("Aloe", "Schistosoma", "Styrene"))
  str(dat2)
}

Extract FEMA from PubChem

Description

This function retrieves FEMA (Flavor and Extract Manufacturers Association) flavor profile information for a list of CAS Registry Numbers (CASRN) from the PubChem database using the webchem package. It applies the function extr_fema_pubchem_ to each CASRN in the input vector and combines the results into a single data frame.

Usage

extr_pubchem_fema(casrn, verbose = TRUE)
extr_pubchem_fema(casrn, verbose = TRUE)

Arguments

`casrn`	A vector of CAS Registry Numbers (CASRN) as atomic vectors.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A data frame containing the FEMA flavor profile information for each CASRN. If no information is found for a particular CASRN, the output will include a row indicating this.

Examples


extr_pubchem_fema(c("83-67-0", "1490-04-6"))

extr_pubchem_fema(c("83-67-0", "1490-04-6"))

Extract GHS Codes from PubChem

Description

This function extracts GHS (Globally Harmonized System) codes from PubChem. It relies on the webchem package to interact with PubChem.

Usage

extr_pubchem_ghs(casrn, verbose = TRUE)
extr_pubchem_ghs(casrn, verbose = TRUE)

Arguments

`casrn`	Character vector of CAS Registry Numbers (CASRN).
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Value

A dataframe containing GHS information.

Examples


extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5"))

extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5"))

Extract Tetramer Data from the CTD API

Description

This function queries the Comparative Toxicogenomics Database API to retrieve tetramer data based on chemicals, diseases, genes, or other categories.

Usage

extr_tetramer(
  chem,
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals",
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)
extr_tetramer(
  chem,
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals",
  verify_ssl = FALSE,
  verbose = TRUE,
  ...
)

Arguments

`chem`	A string indicating the chemical identifiers such as CAS number or IUPAC name of the chemical.
`disease`	A string indicating a disease term. Default is an empty string.
`gene`	A string indicating a gene symbol. Default is an empty string.
`go`	A string indicating a Gene Ontology term. Default is an empty string.
`input_term_search_type`	A string specifying the search method to use. Options are "hierarchicalAssociations" or "directAssociations". Default is "directAssociations".
`qt_match_type`	A string specifying the query type match method. Options are "equals" or "contains". Default is "equals".
`verify_ssl`	Boolean to control if SSL should be verified or not. Default is FALSE.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.
`...`	Any other arguments to be supplied to `req_option` and thus to `libcurl`.

Value

A data frame containing the queried tetramer data in CSV format.

References

Comparative Toxicogenomics Database: http://ctdbase.org
Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, T. C., & Mattingly, C. J. (2019). The Comparative Toxicogenomics Database: update 2019. Nucleic acids research, 47(D1), D948–D954. doi:10.1093/nar/gky868
Davis, A. P., Wiegers, T. C., Wiegers, J., Wyatt, B., Johnson, R. J., Sciaky, D., Barkalow, F., Strong, M., Planchart, A., & Mattingly, C. J. (2023). CTD tetramers: A new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health. Toxicological Sciences, 195(2), 155–168. doi:10.1093/toxsci/kfad069

Examples


tetramer_data <- extr_tetramer(
  chem = c("50-00-0", "ethanol"),
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals"
)
str(tetramer_data)

tetramer_data <- extr_tetramer(
  chem = c("50-00-0", "ethanol"),
  disease = "",
  gene = "",
  go = "",
  input_term_search_type = "directAssociations",
  qt_match_type = "equals"
)
str(tetramer_data)

Extract Toxicological Information from Multiple Databases

Description

This wrapper function retrieves toxicological information for specified chemicals by calling several external functions to query multiple databases, including PubChem, the Integrated Chemical Environment (ICE), CompTox Chemicals Dashboard, and the Integrated Risk Information System (IRIS).

Usage

extr_tox(casrn, verbose = TRUE)
extr_tox(casrn, verbose = TRUE)

Arguments

`casrn`	A character vector of CAS Registry Numbers (CASRN) representing the chemicals of interest.
`verbose`	A logical value indicating whether to print detailed messages. Default is TRUE.

Details

Specifically, this function:

Calls extr_monograph to return monographs informations from WHO IARC.
Calls extr_pubchem_ghs to retrieve GHS classification data from PubChem.
Calls extr_ice to gather assay data from the ICE database.
Calls extr_iris to retrieve risk assessment information from the IRIS database.
Calls extr_comptox to retrieve data from the CompTox Chemicals Dashboard.

Value

A list of data frames containing toxicological information retrieved from each database:

who_iarc_monographs: Lists if any, the WHO IARC monographs related to that chemical.
ghs_dat: Toxicity data from PubChem's Globally Harmonized System (GHS) classification.
ice_dat: Assay data from the Integrated Chemical Environment (ICE) database.
iris: Risk assessment data from the IRIS database.
iris: Risk assessment data from the IRIS database.
comptox_list: List of dataframe with toxicity information from the CompTox Chemicals Dashboard.

Examples


extr_tox(casrn = c("100-00-5", "107-02-8"))

extr_tox(casrn = c("100-00-5", "107-02-8"))

Write Dataframes to Excel

Description

This function creates an Excel file with each dataframe in a list as a separate sheet.

Usage

write_dataframes_to_excel(df_list, filename)
write_dataframes_to_excel(df_list, filename)

Arguments

`df_list`	A named list of dataframes to write to the Excel file.
`filename`	The name of the Excel file to create.

Value

No return value. The function prints a message indicating the completion of the Excel file writing.

Examples


tox_dat <- extr_tox("50-00-0")
temp_file <- tempfile(fileext = ".xlsx")
write_dataframes_to_excel(tox_dat, filename = temp_file)

tox_dat <- extr_tox("50-00-0")
temp_file <- tempfile(fileext = ".xlsx")
write_dataframes_to_excel(tox_dat, filename = temp_file)

Package 'extractox'

Help Index

Retrieve CASRN for PubChem CIDs

Description

Usage

Arguments

Value

See Also

Examples

Query Chemical Information from IUPAC Names

Description

Usage

Arguments

Value

Examples

Download and Extract Data from CompTox Chemistry Dashboard

Description

Usage

Arguments

Details

Value

See Also

Examples

Extract Data from the CTD API

Description

Usage

Arguments

Value

References

See Also

Examples

Extract Data from NTP ICE Database

Description

Usage

Arguments

Value

See Also

Examples

Extract Assay Names from the ICE Database

Description

Usage

Arguments

Value

Examples

Extract Data from EPA IRIS Database

Description

Usage

Arguments

Value

See Also

Examples

Retrieve WHO IARC Monograph Information

Description

Usage

Arguments

Value

See Also

Examples

Extract FEMA from PubChem

Description

Usage

Arguments

Value

See Also

Examples

Extract GHS Codes from PubChem

Description

Usage

Arguments

Value

See Also

Examples

Extract Tetramer Data from the CTD API

Description

Usage

Arguments

Value

References

See Also

Examples