Unfortunately, the BacDive Web Service does not allow SQL-like queries for the content of specific fields within the strain’s datasets. If you find the functionality explained in BacDive-ing in too limited, please try the following, semi-automatic approach to using BacDiveR.

  1. Visit BacDive.DSMZ.de/AdvSearch and prepare the query you are interested in.
Overview of the possible fields to query and their parameters (contains, exact, begins/ends with)

Overview of the possible fields to query and their parameters (contains, exact, begins/ends with)

  1. Run your advanced search (query). In the below example, I simply searched for all strains whose publication includes someone named “Miller”. Note the two “hits” on the right, and the now much longer URL. It contains/encodes all the terms and parameters of your advanced search.
Advanced search results

Advanced search results

  1. Copy the URL of the results page from your browser’s adress bar. Alternatively, copy it from the “Download list of BacDive Ids” link to the top right of the “hits” list.

  2. Paste the copied URL into a call to the retrieve_search_results() function.

  3. Enjoy the list of downloaded datasets, just as you would after using retrieve_data(searchTerm = ..., searchType = ...).