BacDiveR: Programmatic Interface For The DSMZ' Bacterial Diversity Metadatabase
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 replaceretrieve_data()
soon. It consists ofbd_retrieve(id = …)
,bd_retrieve_by_culture(collectionno = …)
,bd_retrieve_by_sequence(accession = …)
andbd_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 tobd_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
- Is supplement to
- https://github.com/TIBHannover/BacDiveR/tree/0.8.0 (URL)