Planned intervention: On Wednesday April 3rd 05:30 UTC Zenodo will be unavailable for up to 2-10 minutes to perform a storage cluster upgrade.

There is a newer version of the record available.

Published February 23, 2019 | Version 0.8.0
Software Open

BacDiveR: Programmatic Interface For The DSMZ' Bacterial Diversity Metadatabase

  • 1. @TIBHannover

Description

This R package provides a programmatic interface to the Bacterial Diversity Metadatabase of the DSMZ (German Collection of Microorganisms and Cell Cultures). BacDiveR helps you improve your research on bacteria and archaea by providing access to "structured information on [...] their taxonomy, morphology, physiology, cultivation, geographic origin, application, interaction" and more (Söhngen et al. 2016). Specifically, you can:

  • download the BacDive data you need for offline investigation, and

  • document your searchers and downloads in .R scripts, .Rmd files, etc.

Thus, BacDiveR can be the basis for a reproducible data analysis pipeline. See TIBHannover.GitHub.io/BacDiveR for more details, /news there for the changelog, and GitHub.com/TIBHannover/BacDiveR for the latest source code.

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

Changelog for BacDiveR 0.8.0

Added

  • NEW API: The bd_retrieve() family of functions will replace retrieve_data() soon. It consists of bd_retrieve(id = …), bd_retrieve_by_culture(collectionno = …), bd_retrieve_by_sequence(accession = …) and bd_retrieve_taxon(name = …) which is more auto-complete-friendly and should help avoid the internal need to sanitise inputs.

Deprecated

  • retrieve_data() has been replaced as described above.
  • retrieve_search_results() has been renamed to bd_retrieve_by_search().
  • Both old functions will be removed in the next major version. Please update your BacDiveR-using scripts and other downstream code.

Files

TIBHannover/BacDiveR-0.8.0.zip

Files (1.1 MB)

Name Size Download all
md5:cee6e2ab4f9446171ec78f2941e23cab
1.1 MB Preview Download

Additional details

Related works