Introduction

In this vignette, CTX Chemical API will be explored.

The foundation of toxicology, toxicokinetics, and exposure is embedded in the physics and chemistry of chemical-biological interactions. The accurate characterization of chemical structure linked to commonly used identifiers, such as names and Chemical Abstracts Service Registry Numbers (CASRNs), is essential to support both predictive modeling of the data as well as dissemination and application of the data for chemical safety decisions.

With cheminformatics as the backbone for research efforts, sources of available data through the CTX Chemical API include:

• Chemical structures, nomenclature, synonyms, IDs, list associations, physicochemical property, environmental fate and transport data from the Distributed Structure-Searchable Toxicity (DSSTox) database. DSSTox substance identifiers (DTXSIDs) support linking chemical information to a specific chemical across a variety of EPA chemical resources. For early references, see (Richard, A. et al. 2002), (Richard, A. et al. 2006), and (Richard, A. et al 2008).
• Predictions from Toxicity Estimation Software Tool (TEST) suite of QSAR models. For early references, see (Martin, T. et al. 2001), (Martin, T. et al. 2007), and (Young, D. et al. 2008).

More information on Chemicals and Chemistry Data can be found here: https://www.epa.gov/comptox-tools/downloadable-computational-toxicology-data#SCD.

Several ctxR functions can be used to access the CTX Chemical API data, as described in the following sections.Tables output in each example have been filtered to only display the first few rows of data.

Chemical Details Resource

chemical_details_by_dtxsid <- get_chemical_details(DTXSID = 'DTXSID7020182')

chemical_details_by_dtxcid <- get_chemical_details(DTXCID = 'DTXCID30182')

vector_dtxsid<- c("DTXSID7020182", "DTXSID9020112", "DTXSID8021430")
chemical_details_by_batch_dtxsid <- get_chemical_details_batch(DTXSID = vector_dtxsid)

vector_dtxcid <- c("DTXCID30182", "DTXCID801430", "DTXCID90112")
chemical_details_by_batch_dtxcid <- get_chemical_details_batch(DTXCID = vector_dtxcid)

Pubchem Link to GHS classification

dtxsid_check_true <- check_existence_by_dtxsid(DTXSID = 'DTXSID7020182')
dtxsid_check_false <- check_existence_by_dtxsid(DTXSID = 'DTXSID7020182f')

vector_dtxsid_and_non_dtxsid <- c('DTXSID7020182F', 'DTXSID7020182', 'DTXSID0020232F')
dtxsid_checks <- check_existence_by_dtxsid_batch(DTXSID = vector_dtxsid_and_non_dtxsid)

Chemical Property Resource

get_chemical_by_property_range() retrieves data for chemicals that have a specified property within the input range.

chemical_by_property_range <- get_chemical_by_property_range(start = 1.311, 
                                         end = 1.313, 
                                         property = 'Density')

get_chem_info() retrieves specific chemical information for an input chemical. This includes both experimental and predicted values by default, but providing “experimental” or “predicted” to the type parameter will return the specific associated information.

chemical_info <- get_chem_info(DTXSID = 'DTXSID7020182')

Chemical Fate Resource

get_fate_by_dtxsid() retrieves chemical fate data.

fate_by_dtxsid <- get_fate_by_dtxsid(DTXSID = 'DTXSID7020182')

Chemical Search Resource

Chemicals can be searched using string values. These values can be a chemical name, DTXSID, DTXCID, CAS Registry Number (CASRN), or InChIKey. Examples for each are provided by the following:

search_starts_with_dtxsid <- chemical_starts_with(word = 'DTXSID7020182')
search_starts_with_chem_name <- chemical_starts_with(word = 'Bisph')
search_starts_with_casrn <- chemical_starts_with(word = '80-05-7')
search_starts_with_inchikey <- chemical_starts_with(word = 'IISBACLAFKSPIT')

search_exact_dtxsid <- chemical_equal(word = 'DTXSID7020182')
search_exact_chem_name <- chemical_equal(word = 'Bisphenol A')
search_exact_casrn <- chemical_equal(word = '80-05-7')
search_exact_inchikey <- chemical_equal(word = 'IISBACLAFKSPIT-UHFFFAOYSA-N')

search_contains_dtxsid <- chemical_contains(word = 'DTXSID702018')
search_contains_chem_name <- chemical_contains(word = 'Bisph')
search_contains_casrn <- chemical_contains(word = '80-05-7')
search_contains_inchikey <- chemical_contains(word = 'IISBACLAF')

msready_by_mass <- get_msready_by_mass(start = 200.9, 
                              end = 200.95)

msready_by_formula <- get_msready_by_formula(formula = 'C16H24N2O5S')

msready_by_dtxcid <- get_msready_by_dtxcid(DTXCID = 'DTXCID30182')

List Resource

There are several lists of chemicals one can access using the CCD list search. These can be filtered by the type, name, inclusion of a specific chemical, or name of list.

get_all_list_types()

chemical_lists_by_type <- get_chemical_lists_by_type(type =  'federal')

public_chemical_list_by_name <- get_public_chemical_list_by_name(listname = 'CCL4')

lists_containing_chemical <- get_lists_containing_chemical(DTXSID = 'DTXSID7020182')

chemicals_in_ccl4_start <- get_chemicals_in_list_start(list_name = 'CCL4', word = 'Bi')

chemicals_in_ccl4_exact <- get_chemicals_in_list_exact(list_name = 'BIOSOLIDS2021', word = 'Bisphenol A')

chemicals_in_ccl4_contain <- get_chemicals_in_list_contain(list_name = 'CCL4', word = 'Bis')

chemicals_in_list <- get_chemicals_in_list(list_name = 'CCL4')

Chemical File Resource

There are mrv, mol, and image files that can be accessed using either the DTXSID or DTXCID. Examples are provided below:

chemical_mrv_by_dtxsid <- get_chemical_mrv(DTXSID = 'DTXSID7020182')
chemical_mrv_by_dtxcid <- get_chemical_mrv(DTXCID = 'DTXCID30182')

chemical_mol_by_dtxsid <- get_chemical_mol(DTXSID = 'DTXSID7020182')
chemical_mol_by_dtxcid <- get_chemical_mol(DTXCID = 'DTXCID30182')

chemical_image_by_dtxsid <- get_chemical_image(DTXSID = 'DTXSID7020182')
chemical_image_by_dtxcid <- get_chemical_image(DTXCID = 'DTXCID30182')
chemical_image_by_smiles <- get_chemical_image(SMILES = 'CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1')

countcolors::plotArrayAsImage(chemical_image_by_dtxsid)
countcolors::plotArrayAsImage(chemical_image_by_dtxcid)
countcolors::plotArrayAsImage(chemical_image_by_smiles)

Chemical Synonym Resource

get_chemical_synonym() retrieves synonyms for the specified chemical.

chemical_synonym <- get_chemical_synonym(DTXSID = 'DTXSID7020182')

Conclusion

In this vignette, a variety of functions that access different types of data found in the Chemical endpoints of the CTX APIs were explored. While this exploration was not exhaustive, it provides a basic introduction to how one may access data and work with it. Additional endpoints and corresponding functions exist and we encourage the user to explore these while keeping in mind the examples contained in this vignette.