On the various yaml files#

Bionty tracks all supported and the currently active ontologies four *.yaml files.

  1. versions.yaml: Stores all by Bionty supported ontologies. Users should not edit this file.

  2. local.yaml: Stores all locally available ontologies. Users may edit this file. The file is stored at $home:/.lamin/bionty.

  3. ._current.yaml: Stores the currently active ontologies. Users should not edit this file.

  4. ._lndb.yaml: Stores the currently active ontologies as defined by lamindb. Users should never edit this file directly.

On startup, Bionty syncs these yaml files. If Bionty is used for the first time the local.yaml file gets populated by the versions available in the most recent versions.yaml. Afterwards, the ._current.yaml file containing the current default versions gets written using the versions that are at the top of the ._local.yaml file. If the user is operating in a lamindb instance, the versions specified in the ._lndb.yaml will be used. Alternatively, if Bionty is run in standalone mode, the versions specified in ._current.yaml will be used. Users may adapt the local.yaml with additional sources of ontologies that Bionty may not offer out of the box.

The available and currently active ontologies can also be printed to the console with bionty.display_available_versions() or bionty.display_active_versions().

Setting default ontologies and versions#

Since the default ontologies and versions are stored in the ._current.yaml or the ._lndb.yaml respectively, we can use bionty.update_defaults() to set new defaults.