Configuration

Public bionty sources

Bionty maintains a sources.yaml listing public sources of each entity. These sources are curated (bionty-assets) and stored in a bionty-assets instance to provide fast and reliable access. Cached sources files are stored at your local bionty/base/_dynamic/ directory.

Display public sources

The available and currently used ontologies can also be printed with bionty.base.display_available_sources or bionty.base.display_currently_used_sources.

Structure of the sources.yaml

entity: # Bionty entity class name, e.g. CellType
  source: # short name of the source, (CURIE prefix for ontologies) e.g. cl
    organism: # organism common name, (if none applied, use 'all') e.g. human
      version: # version of the source
        url: # "link to the source file"

Default ontologies and versions in sources.yaml

For each entity, the first source and its maximum version defined in sources.yaml is used as default. To set your own default ontology and version, shift the order of entries. For example, in the following “doid” used when “organism” is specified as “human”:

(highlighted sources are considered the default)

Disease:
  mondo:
    all:
      2023-02-06:
        source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
    name: Mondo Disease Ontology
    website: https://mondo.monarchinitiative.org/
  doid:
    human:
      2023-01-30:
        source: http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo
    name: Human Disease Ontology
    website: https://disease-ontology.org/
  inhouse_diseases:
    human:
      2000-01-01:
        source: http://download-my-diseases.com/releases/2000-01-01/mydiseases.owl
    name: My in-house Disease Ontology
    website: http://my-website.com

We may change the default to “inhouse_diseases” when “organism” is specified as “human”, by the following:

Disease:
  mondo:
    all:
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
      2023-02-06:
        source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl
    name: Mondo Disease Ontology
    website: https://mondo.monarchinitiative.org/
  inhouse_diseases:
    human:
      2000-01-01:
        source: http://download-my-diseases.com/releases/2000-01-01/mydiseases.owl
    name: My in-house Disease Ontology
    website: http://my-website.com
  doid:
    human:
      2023-01-30:
        source: http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo
    name: Human Disease Ontology
    website: https://disease-ontology.org/