This R package provides a programmatic interface for the Bacterial Diversity Metadatabase (Söhngen et al. 2014 & 2016) of the DSMZ (German Collection of Microorganisms and Cell Cultures). BacDiveR helps you to conduct your microbial research better and faster, by:
downloading the BacDive datasets you want to investigate off-line, and by
providing you with a way to document and report your searches and downloads, in a reproducible manner (.R
scripts and/or .Rmd
files).
Because the BacDive API requires registration please do that first and wait for your access to be granted.
Once you have your login credentials, install BacDiveR from GitHub with:
# install.packages("devtools")
In the examples and vignettes, the data retrieval will only work if your login credentials are correct in themselves (no typos) and were correctly saved. Console output like "{\"detail\": \"Invalid username/password\"}"
, or Error: $ operator is invalid for atomic vectors
indicate that either the login credentials are incorrect, or the .Renviron
file. In that case, please run:
file.edit(file.path(Sys.getenv('HOME'), '.Renviron'))
and make sure it contains the following:
BacDive_email=your.email@provider.org
BacDive_password=YOUR_20_char_password
There are two main functions. Please click on their names to read their docu: retrieve_data()
and retrieve_search_results()
. For real-life examples, please read the vignettes “BacDive-ing in” and about the “Semi-automatic approach”.
Söhngen, Carola, Boyke Bunk, Adam Podstawka, Dorothea Gleim, and Jörg Overmann. 2014. “BacDive—the Bacterial Diversity Metadatabase.” Nucleic Acids Research 42 (D1): D592–D599. doi:10.1093/nar/gkt1058.
Söhngen, Carola, Adam Podstawka, Boyke Bunk, Dorothea Gleim, Anna Vetcininova, Lorenz Christian Reimer, Christian Ebeling, Cezar Pendarovski, and Jörg Overmann. 2016. “BacDive – the Bacterial Diversity Metadatabase in 2016.” Nucleic Acids Research 44 (D1): D581–D585. doi:10.1093/nar/gkv983.