How to download the full database

[zji90]

Hi,

I wonder whether there is a way to download the full BacDive database without doing the search? Thanks!

[katrinleinweber]

Hi @zji90 👋 It's probably best to contact the official BacDive team about that.

From my outside observation (now almost 2 years ago), I think there are 2 options in which BacDiveR can help you unofficially:

1. Iterating up from bd_retrieve(id = 1) to (currently 82892), with a reasonable wait time in between (half a second?) and some client-side catching/skipping of errors (some IDs were nonexistent).
2. Mass-downloading datasets with a few very general search queries, like Domain contains Bacteria and Domain contains Archaea.

[JackLMc]

For others that found this... This is the reply I received from the BacDive team:

"BacDive is a complex database with over 1000 data fields. Therefore there is no easy way to download the whole database (e.g. as a plain spreadsheet).
We recommend using the API for accessing data for many strains at once. Please have a look. Access is free after registration and we do provide clients for Python and R.

If you a further questions don't hesitate to ask.

Best regards,"

[katrinleinweber]

I wonder why they never contributed to this client, despite seeking cooperation projects with TIB. Case closed then, also because of #118.