refdb_import_BOLD: Download and import BOLD records

View source: R/import_BOLD.R

refdb_import_BOLDR Documentation

Download and import BOLD records


This function allows to search and download data from the the BOLD database. Additionally it allows to convert the BOLD taxonomic classification into the NCBI classification using the NCBI Taxonomy database.


  taxon = NULL,
  ids = NULL,
  bin = NULL,
  container = NULL,
  institutions = NULL,
  researchers = NULL,
  geo = NULL,
  ncbi_taxo = TRUE,
  full = FALSE,
  verbose = TRUE


taxon, ids, bin, container, institutions, researchers, geo

terms used to search the BOLD database. See bold_seqspec from which they are inherited.


if TRUE (the default) the BOLD taxonomy is replaced by the NCBI taxonomy using refdb_set_ncbitax.


if TRUE the complete data are returned for every records. If FALSE (the default) only a subset of the most important columns is returned.


print information in the console.


This function uses several functions of the bold package to interface with the BOLD API. The NCBI Taxonomy database is queried using the rentrez package.


A tibble.

Large requests

As detailed in the manual of bold_seqspec, some large requests (e.g. high ranked taxa) can lead to errors. In that case one strategy can be to sequentially download data for lower rank taxa. See

See Also

link[bold]bold_stats and bold_seqspec from bold which are used internally.


## Not run: 
goera_bold <- refdb_import_BOLD(taxon = "Goera pilosa", ncbi_taxo = FALSE)

## End(Not run)

refdb documentation built on Sept. 22, 2022, 5:07 p.m.