What's the current version for each biological database?
A daily updated static listing of all current versions (that are incorporated) can be found at https://biopragmatics.github.io/bioversions.
$ pip install bioversions
import bioversions assert bioversions.get_version('biogrid') == '4.2.192', 'This was true on Dec 5th, 2020!' # If you want more information, use the resolve() function bioversion = bioversions.resolve('biogrid') assert bioversion.version == '4.2.192'
By default, the results are cached and only refreshed once per day with the help
cachier. The cache is stored in
~/.data/bioversions. The cache location
can be overridden by setting the
BIOVERSIONS_HOME environment variable via
🌐 Web Application
While https://biopragmatics.github.io/bioversions provides a daily updated static listing of the database, you can run a dynamic version with an API from your shell with:
$ bioversions web
Options can be listed with
bioversions web --help.
You can navigate to http://localhost:5000 to see all versions as HTML or programmatically resolve given databases with
http://localhost:5000/database/<name> endpoint like in the following:
import requests res = requests.get('http://localhost:5000/database/biogrid').json() assert res['success'] assert res['result']['name'] == 'BioGRID' assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'
You can use
bioversions get to incorporate the latest versions in your shell scripts or REPL usage like in:
$ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
To add more databases to the list, you can create a new submodule of
bioversions.sources and extend the
bioversions.utils.Getter class to identify the most recent version for your
target database. See
bioversions.sources.biogrid as an example.
Code is licensed under the MIT License.
The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).