Retrieve (a) Dataset(s) from BacDive

Source: R/bd_retrieve.R, R/bd_retrieve_by_culture.R, R/bd_retrieve_by_sequence.R, and 2 more

Retrieve (a) Dataset(s) from BacDive

bd_retrieve(id)

bd_retrieve_by_culture(collection_no)

bd_retrieve_by_sequence(accession)

bd_retrieve_taxon(name)

Arguments

id

Mandatory character string or integer. The BacDive strain ID whose data you want to retrieve.
collection_no

Mandatory character string. A culture collection number by which the associated dataset(s) will be retrieved.
accession

Mandatory character string. A sequence accession number by which the associated dataset(s) will be retrieved.
name

Mandatory character string, specifying the taxon. Abbreviations like "B. halotolerans" are not allowed!

Value

A (large) list containing either a single BacDive dataset in case your parameter / search was unambiguous, or if ambiguous: all matching datasets. Read BacDive.DSMZ.de/api/bacdive to learn more.

Examples

  dataset_717 <- bd_retrieve(id = 717)
#> 717 
  dataset_717 <- bd_retrieve(id = "717")
#> 717 
  dataset_DSM_319 <- bd_retrieve_by_culture(collection_no = "DSM 319")
#> 20319 
#> 717 
  dataset_AJ000733 <- bd_retrieve_by_sequence(accession = "AJ000733")
#> 000733 
#> 717 
  datasets_Bh <- bd_retrieve_taxon(name = "Bacillus halotolerans")
#>  
#> Downloading BacDive IDs 1095 to 136272 (but not necessarily contiguously): 
#> 1095 
#> 1847 
#> 134137 
#> 135375 
#> 135398 
#> 135750 
#> 136272 
  datasets_Thh <- bd_retrieve_taxon(name = "Tetragenococcus halophilus halophilus")
#>  
#> Downloading BacDive IDs 5253 to 5255 (but not necessarily contiguously): 
#> 5253 
#> 5254 
#> 5255