Export a map_concepts result as a JSON document — mapping_to

Converts the data.frame returned by map_concepts into a JSON document. Terms are grouped by ontology; each entry records the ontology IRI, term label, OBO identifier, and the input concept that was mapped.

Usage

mapping_to_json(x, validated_only = TRUE, path = NULL)

Arguments

x: data.frame as returned by map_concepts.
validated_only: logical(1) if TRUE (default), only rows where validated == TRUE are included.
path: character(1) or NULL. When not NULL, the JSON is written to this file path and NULL is returned invisibly. When NULL (default) the JSON string is returned.

Value

A JSON character string, or NULL invisibly when path is supplied.

Examples

df <- data.frame(
  input_text = c("atrial fibrillation", "genome sequencing"),
  term_label = c("Atrial Fibrillation", "Whole Genome Sequencing"),
  term_iri   = c("http://purl.obolibrary.org/obo/HP_0005110",
                 "http://purl.obolibrary.org/obo/OBI_0002117"),
  obo_id     = c("HP:0005110", "OBI:0002117"),
  ontology   = c("HP", "OBI"),
  rationale  = c("matches concept", "matches concept"),
  validated  = c(TRUE, TRUE),
  definition = c(NA_character_, NA_character_),
  stringsAsFactors = FALSE
)
cat(mapping_to_json(df))
#> {
#>   "HP": [
#>     {
#>       "input_text": "atrial fibrillation",
#>       "term_label": "Atrial Fibrillation",
#>       "term_iri": "http://purl.obolibrary.org/obo/HP_0005110",
#>       "obo_id": "HP:0005110"
#>     }
#>   ],
#>   "OBI": [
#>     {
#>       "input_text": "genome sequencing",
#>       "term_label": "Whole Genome Sequencing",
#>       "term_iri": "http://purl.obolibrary.org/obo/OBI_0002117",
#>       "obo_id": "OBI:0002117"
#>     }
#>   ]
#> }