Retrieve data from BacDive

retrieve_data(searchTerm, searchType = "taxon")

Arguments

searchTerm

Mandatory character string (in case of searchType = sequence, culturecollectionno or taxon) or integer (in case of bacdive_id), specifying what shall be searched for.

searchType

Mandatory character string that specifies which type of search will be performed (technically, which API endpoint). Can be taxon (default), bacdive_id, sequence, or culturecollectionno.

Value

A list of lists containing either a single BacDive dataset in case the searchTerm was unambiguous (bacdive_id, sequence, culturecollectionno), or a large list containing all datasets that match an ambiguous searchTerm (most taxons).

Examples

dataset <- retrieve_data(searchTerm = 717, searchType = "bacdive_id")
#> 717
# dataset <- retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno") # dataset <- retrieve_data(searchTerm = "AJ000733", searchType = "sequence") # Bss_data <- retrieve_data(searchTerm = "Bacillus subtilis subtilis")