extractox is a comprehensive R package designed to simplify querying
various chemical, toxicological, and biological databases such as the
Comparative Toxicogenomics Database (CTP) of the MDI Biological
Laboratory and NC State University, the Integrated Chemical Environment
(ICE) of the National Toxicology Program (NTP), the Integrated Risk
Information System (IRIS) of the Environmental Protection Agency (EPA),
the CompTox Chemicals Dashboard Resource Hub (CompTox) of EPA, and
PubChem of the National Center for Biotechnology Information/National
Institures Of Health (NCBI, NIH). The package facilitates interaction
with APIs, providing curated and user-friendly outputs.
To communicate with Pubchem, extractox relies on the packagewebchem.
Install the package extractox from CRAN.
# From CRAN
install.packages("extractox")
To get a bug fix or to use a feature from the development version, you
can install the development version of extractox from GitHub.
# Install pak if not already installed
if (!requireNamespace("pak", quietly = TRUE)) {
install.packages("pak")
}
# Install the package from GitHub
pak::pkg_install("c1au6i0/extractox")
The ICE database, managed by the EPA, provides access to a variety of data related to chemical toxicity, exposure, and risk assessment. It includes data from high-throughput screening assays, in vivo studies, and computational models.
extr_ice provides access to NTP’s ICE database for toxicological and
exposure-related data.
library(extractox)
ice_data <- extr_ice(casrn = c("50-00-0"), assays = NULL) # assays is null so all assays are retrieved
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Sending request to ICE database...
#> Request succeeded with status code: 200
names(ice_data)
#> [1] "assay" "endpoint" "substanceType"
#> [4] "casrn" "qsarReadyId" "value"
#> [7] "unit" "species" "receptorSpecies"
#> [10] "route" "sex" "strain"
#> [13] "lifeStage" "tissue" "lesion"
#> [16] "location" "assaySource" "inVitroAssayFormat"
#> [19] "reference" "referenceUrl" "dtxsid"
#> [22] "substanceName" "pubMedId"
There are more than 2000 possible assays in ICE. The
extr_ice_assay_names() function allows to search for assay names that
match a pattern you’re interested in. Please note that searches are case
sensitive and accept regexp.
extr_ice_assay_names("Rat Acute") # keep empty to retrieve all
#> [1] "Rat Acute Oral Toxicity" "Rat Acute Inhalation Toxicity"
#> [3] "Rat Acute Dermal Toxicity" "CATMoS, Rat Acute Oral Toxicity"
The IRIS database is managed by the EPA and contains information on the health effects of exposure to various substances found in the environment. It provides qualitative and quantitative health risk information.
extr_iris provides access to EPA’s IRIS database and accepts queries
of Chemical Abstracts Service Registry Number (CASRN) or International
Union of Pure and Applied Chemistry (IUPAC) names of chemicals.
iris_info <- extr_iris(c("glyphosate", "50-00-0"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Quering glyphosate to EPA IRIS database...
#> Request succeeded with status code: 200
#> Quering 50-00-0 to EPA IRIS database...
#> Request succeeded with status code: 200
names(iris_info)
#> [1] "chemical_name" "casrn"
#> [3] "exposure_route" "assessment_type"
#> [5] "critical_effect_or_tumor_type" "woe_characterization"
#> [7] "toxicity_value_type" "toxicity_value"
The CompTox Chemistry Dashboard, managed by the EPA, provides access to data on chemical structures, properties, and associated bioactivity data. It integrates data from various sources to support chemical safety assessments.
extr_comptox extracts data from the CompTox Chemistry Dashboard using
both CASRN and IUPAC names of chemicals and returns a list of
dataframes.
info_comptox <- extr_comptox(ids = c("Aspirin", "50-00-0"))
#> ℹ Sending request to CompTox...
#> Request succeeded with status code: 202
#> ℹ Getting info from CompTox...
#>
#> Request succeeded with status code: 200
names(info_comptox)
#> [1] "comptox_cover_sheet" "comptox_main_data"
#> [3] "comptox_abstract_sifter" "comptox_synonym_identifier"
#> [5] "comptox_related_relationships" "comptox_toxcast_assays_ac50"
#> [7] "comptox_toxval_details" "comptox_chemical_properties"
The function extr_tox is a wrapper used to call all the
above-mentioned functions and retrieve a list of dataframes.
info_tox <- extr_tox(casrn = c("Aspirin", "50-00-0"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> ℹ Getting PubChem IDS...
#> Querying Aspirin. OK (HTTP 200).
#> Querying 2244. OK (HTTP 200).
#> ℹ Getting PubChem IDS...
#> Querying 50-00-0. OK (HTTP 200).
#> Querying 712. OK (HTTP 200).
#> ℹ Sending request to CompTox...
#> Request succeeded with status code: 202ℹ Getting info from CompTox...
#> Request succeeded with status code: 200ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Sending request to ICE database...Request succeeded with status code: 200ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Quering Aspirin to EPA IRIS database...Request succeeded with status code: 200Quering 50-00-0 to EPA IRIS database...Request succeeded with status code: 200
The CTP provides information about the interactions between chemicals, genes, and diseases. It helps in understanding the effects of environmental exposures on human health.
A series of functions interact with the CTP database.
extr_ctd extracts information related to chemical-gene or pathway
associations.
input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol")
ctd_association <- 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")
)
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Sending request to CTD database...
#> Request succeeded with status code: 200
# Get expresssion data
ctd_expression <- extr_ctd(
input_terms = input_terms,
report_type = "cgixns",
category = "chem",
action_types = "expression"
)
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Sending request to CTD database...Request succeeded with status code: 200
names(ctd_expression)
#> [1] "x_input" "chemical_name" "chemical_id"
#> [4] "cas_rn" "gene_symbol" "gene_id"
#> [7] "organism" "organism_id" "interaction"
#> [10] "interaction_actions" "pub_med_i_ds"
Tetramers are computationally generated information units that interrelate four data types from the CTP: a chemical, gene product, phenotype, and disease. They help in understanding the complex relationships between these entities and their combined impact on human health.
extr_tetramer extract info related to tetramers from CTD.
tetramer_data <- extr_tetramer(
chem = c("50-00-0", "ethanol"),
disease = "",
gene = "",
go = "",
input_term_search_type = "directAssociations",
qt_match_type = "equals"
)
#> Sending request to CTD database for tetramer data for 50-00-0...
#> Request succeeded with status code: 200
#> Sending request to CTD database for tetramer data for ethanol...
#> Request succeeded with status code: 200
names(tetramer_data)
#> [1] "query" "chemical" "chemical_id" "gene" "gene_id"
#> [6] "phenotype" "phenotype_id" "disease" "disease_id"
PubChem is an open chemistry database at the NIH. It provides information on chemical structures, identifiers, chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations, and more.
A series of functions that rely on the webchem package are used to
extract chemical information, Globally Harmonized System (GHS)
classification data, or flavor classification from PubChem.
The function extr_chem_info retrieves chemical information of
IUPAC-named chemicals. A warning is displayed if the chemical is not
found.
chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Querying Formaldehyde. OK (HTTP 200).
#> Querying Aflatoxin B1. OK (HTTP 200).
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> ℹ Querying 712 and 186907.
names(chem_info)
#> [1] "cid" "iupac_name"
#> [3] "cas_rn" "cid_all"
#> [5] "cas_rn_all" "molecular_formula"
#> [7] "molecular_weight" "canonical_smiles"
#> [9] "isomeric_smiles" "in_ch_i"
#> [11] "in_ch_i_key" "iupac_name_y"
#> [13] "x_log_p" "exact_mass"
#> [15] "monoisotopic_mass" "tpsa"
#> [17] "complexity" "charge"
#> [19] "h_bond_donor_count" "h_bond_acceptor_count"
#> [21] "rotatable_bond_count" "heavy_atom_count"
#> [23] "isotope_atom_count" "atom_stereo_count"
#> [25] "defined_atom_stereo_count" "undefined_atom_stereo_count"
#> [27] "bond_stereo_count" "defined_bond_stereo_count"
#> [29] "undefined_bond_stereo_count" "covalent_unit_count"
#> [31] "volume3d" "x_steric_quadrupole3d"
#> [33] "y_steric_quadrupole3d" "z_steric_quadrupole3d"
#> [35] "feature_count3d" "feature_acceptor_count3d"
#> [37] "feature_donor_count3d" "feature_anion_count3d"
#> [39] "feature_cation_count3d" "feature_ring_count3d"
#> [41] "feature_hydrophobe_count3d" "conformer_model_rmsd3d"
#> [43] "effective_rotor_count3d" "conformer_count3d"
#> [45] "fingerprint2d" "query"
Two functions are used to extract specific sections of PubChem chemical information using CASRN:
extr_pubchem_ghsextracts Globally Harmonized System (GHS) codes.extr_pubchem_femaextracts flavor profile data.
ghs_info <- extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> ℹ Getting PubChem IDS...
#> Querying 50-00-0. OK (HTTP 200).
#> Querying 712. OK (HTTP 200).
#> ℹ Getting PubChem IDS...
#> Querying 64-17-5. OK (HTTP 200).
#> Querying 702. OK (HTTP 200).
fema_info <- extr_pubchem_fema(casrn = c("50-00-0", "123-68-2"))
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Querying 50-00-0. OK (HTTP 200).
#> Querying 712. Not Found (HTTP 404).
#> ℹ FEMA for 50-00-0 not found!
#> Querying 123-68-2. OK (HTTP 200).
#> Querying 31266. OK (HTTP 200).
Please note that functions that pull data from EPA servers may encounter
issues on some Linux systems. This is because these servers do not
accept secure legacy renegotiation. On Linux system, those functions
depend 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.