Extract Data from the CTD API

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,
  ...
)

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.

...

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

# \donttest{
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")
)
#> ℹ Checking Internet Connection...
#> ℹ Internet connection OK...
#> Sending request to CTD database...
#> Request succeeded with status code: 200
str(dat)
#> 'data.frame':	30106 obs. of  9 variables:
#>  $ x_input      : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
#>  $ chemical_name: chr  "Formaldehyde" "Formaldehyde" "Formaldehyde" "Formaldehyde" ...
#>  $ chemical_id  : chr  "D005557" "D005557" "D005557" "D005557" ...
#>  $ cas_rn       : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
#>  $ gene_symbol  : chr  "A4GALT" "AAK1" "AAMDC" "ABCA11P" ...
#>  $ gene_id      : int  53947 22848 28971 79963 26154 10351 5243 8714 10057 5825 ...
#>  $ organism     : chr  "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
#>  $ organism_id  : int  9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
#>  $ pub_med_ids  : chr  "27664576" "23649840" "23649840" "20655997" ...

# Get expresssion data
dat2 <- 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

str(dat2)
#> 'data.frame':	36112 obs. of  11 variables:
#>  $ x_input            : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
#>  $ chemical_name      : chr  "Formaldehyde" "Formaldehyde" "Formaldehyde" "Formaldehyde" ...
#>  $ chemical_id        : chr  "D005557" "D005557" "D005557" "D005557" ...
#>  $ cas_rn             : chr  "50-00-0" "50-00-0" "50-00-0" "50-00-0" ...
#>  $ gene_symbol        : chr  "A4GALT" "AAK1" "AAMDC" "ABCA11P" ...
#>  $ gene_id            : int  53947 22848 28971 79963 26154 10351 5243 8714 10057 5825 ...
#>  $ organism           : chr  "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
#>  $ organism_id        : int  9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
#>  $ interaction        : chr  "Formaldehyde results in decreased expression of A4GALT mRNA" "Formaldehyde results in increased expression of AAK1 mRNA" "Formaldehyde results in increased expression of AAMDC mRNA" "Formaldehyde results in decreased expression of ABCA11P mRNA" ...
#>  $ interaction_actions: chr  "decreases^expression" "increases^expression" "increases^expression" "decreases^expression" ...
#>  $ pub_med_i_ds       : chr  "27664576" "23649840" "23649840" "20655997" ...
# }

Usage

Arguments

Value

References

See also

Examples