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Export EBI Antibiogram

Source: R/export_ncbi.R
export_ebi_ast.Rd

Format AMRgen long-format AST data to a table with the fields required for submission to EBI, and optionally generate JSON submission files (one per BioSample). See https://www.ebi.ac.uk/amr/amr_submission_guide/).

Usage

export_ebi_ast(
  data,
  pheno_col = "pheno_provided",
  breakpoint_version,
  submission_account,
  domain = "self.ExampleDomain",
  output_dir = NULL
)

Arguments

data

A data frame in AMRgen long format (e.g. output of import_ast() or format_ast()). Expected columns: id, drug_agent, spp_pheno, and at least one phenotype column (see pheno_col). Optional columns: mic, disk, method, platform.

pheno_col

Character string naming the column that contains SIR interpretations (class sir). Default "pheno_provided".

breakpoint_version

Character string specifying the breakpoint version used for interpretation (e.g. "EUCAST 2024").

submission_account

Character string specifying the EBI Webin submission account identifier (e.g. "Webin-###"). If not provided, JSON output files will not be generated and the function will return the formated table only, which can be further updated and converted to submission-ready JSON later using format_ebi_json().

domain

Character string specifying the domain used in the submission metadata (e.g. "self.ExampleDomain"). If not provided, JSON output files will not be generated and the function will return the formated table only, which can be further updated and converted to submission-ready JSON later using format_ebi_json().

output_dir

Character string specifying the directory where JSON files should be written. If not provided, JSON output files will not be generated and the function will return the formated table only, which can be further updated and converted to submission-ready JSON later using format_ebi_json().

Value

Formatted data frame. When output_dir is provided, the AST data is also written to individual JSON submission files, one per BioSample, in the specified directory.

Details

Antibiotic names are in Title Case with "/" separating combination agents (EBI convention, e.g. "Amoxicillin/clavulanic acid").

Species names are derived from the spp_pheno column via AMR::mo_name().

Examples

# Return formatted data frame without writing files
ebi_df <- export_ebi_ast(staph_ast_ebi)
if (FALSE) { # \dontrun{
# Write out data for each BioSample to an individual JSON file for submission
ebi_df <- export_ebi_ast(staph_ast_ebi,
  breakpoint_version = "EUCAST 2015",
  submission_account = "Webin-###",
  domain = "self.ExampleDomain",
  output_dir = "/path/to/output/"
)
} # }