BacDiveR

This package is a work in progress.

A package for downloading data from BacDive, The Bacterial Diversity Metadatabase.

It can be used interactively to fetch data from BacDive given a BacDive ID and a template. An example template is provided in inst/extdata/template.csv to allow some flexibility in adding additional fields without additional functions if you just need the first entry from a particular data point in BacDive.

Requirements

BacDive credentials

Install

devtools::install_github("jwokaty/BacDiveR")
devtools::load_all()

Run

BacDiveR needs your BacDive credentials, which you can set as environment variables

Sys.setenv("BACDIVE_USERNAME"="my_user", "BACDIVE_PASSWORD"="my_pass")

Create an access object

# Setting verbose to FALSE to avoid reminder message
ao <- BacDiveR::authenticate(Sys.getenv("BACDIVE_USERNAME"),
                             Sys.getenv("BACDIVE_PASSWORD"),
                             verbose = FALSE)

Look up by BacDive ID

entry <- BacDiveR::getDataByBacDiveId(ao, id = 132485)
# Default template returns a list with the following data
> names(entry)
 [1] "bacdive_id"                 "taxon_name"                
 [3] "ncbi_id"                    "rank"                      
 [5] "parent_taxon_name"          "parent_ncbi_id"            
 [7] "parent_rank"                "sequence_16S_ncbi_id"      
 [9] "sequence_genome_ncbi_id"    "type_strain"               
 [11] "gram_stain"                 "cell_shape"                
 [13] "motility"                   "hemolysis"                 
 [15] "colony_color"               "incubation_period"         
 [17] "cultivation_medium_used"    "culture_temperature_growth"
 [19] "culture_temperature_type"   "culture_temperature"       
 [21] "culture_temperature_range"  "oxygen_tolerance"          
 [23] "spore_formation"            "halophily"                 
 [25] "metabolite_utiilization"    "metabolite_production"     
 [27] "sample_type"                "geographic_location"       
 [29] "country"                    "biosafety_level"           
 [31] "biosafety_level_comment"    "pathogenicity_human"       
 [33] "pathogenicity_animal"

Save a CSV with all BacDive data based on your template to your working directory

BacDiveR::getData(access_object, verbose = TRUE)