There is a newer version of this record available.

Software Open Access

TIBHannover/BacDiveR v0.5.0-beta

Katrin Leinweber

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 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).

It was also built to serve as a demonstration object during TIB's "FAIR Data & Software" workshop.

See for more details, /news there for the changelog, and for the latest source code.

Changelog for BacDiveR v0.5.0-beta

  • Added syncing of release versions to Zenodo, starting with 10.5281/zenodo.1308061

  • The JSON downloads are no longer purged of all space characters pre-emptively to prevent jsonlite from complaining about invalid encoding (#43). Instead, only \r, \n and \t are repaired to \\r, \\n and \\t, which jsonlite expects. This leads to different output (newline & tabs, where previously only spaces occured)! Thus, if you are parsing BacDiveR output in any way, you may need to adjust that. Because I consider this unlikely given the "maturing" status, and because no API surface was changed, I don't consider this a major change in the sense.

Files (764.2 kB)
Name Size
764.2 kB Download
All versions This version
Views 35436
Downloads 7520
Data volume 65.6 MB15.3 MB
Unique views 20021
Unique downloads 2311


Cite as