Generate EBI antibiogram submission in JSON — format_ebi

Converts the tabular output of export_ebi_ast() into JSON files formatted for submission to EBI as BioSample data (https://www.ebi.ac.uk/amr/amr_submission_guide/). Each row of the input dataset is converted into JSON records and printed to file.

Usage

format_ebi_json(
  ebi_antibiogram_table,
  breakpoint_version,
  submission_account,
  domain = "self.ExampleDomain",
  output_dir
)

Arguments

ebi_antibiogram_table: A data frame in the format output by export_ebi_ast().
breakpoint_version: Character string specifying the breakpoint version used for interpretation (e.g. "EUCAST 2024").
submission_account: Character string specifying the Webin submission account identifier (e.g. "Webin-###").
domain: Character string specifying the domain used in the submission metadata (default "self.ExampleDomain").
output_dir: Character string specifying the directory where JSON files should be written.

Value

Invisibly returns NULL. The function prints JSON-formatted AMR submission records to file.

Details

The function iterates over each biosample in ebi_antibiogram_table and constructs a nested JSON object describing the antimicrobial susceptibility testing result. Each record contains antibiotic metadata, AST standards, measurement values, and resistance phenotype information.

JSON formatting is performed using jsonlite::toJSON() with pretty = TRUE and auto_unbox = TRUE .

Examples

if (FALSE) { # \dontrun{
format_ebi_json(
  ast_dataset,
  breakpoint_version = "EUCAST 2015",
  submission_account = "Webin-###",
  domain = "self.ExampleDomain",
  output_dir = "/path/to/output/"
)
} # }