Generate EBI antibiogram submission in JSON — format_ebi

Converts the tabular output of export_ebi_pheno() 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,
  submission_account,
  output_dir,
  domain = NULL
)

Arguments

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

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,
  submission_account = "Webin-###",
  output_dir = "/path/to/output/"
)
} # }