Configuration

Public bionty sources

Bionty maintains a sources.yaml listing public sources of each entity.

These sources are curated (biony-assets) and stored at s3://bionty-assets to provide fast and reliable access.

Cached sources files are stored at your local bionty/bionty/_dynamic/ directory.

Local bionty sources

File $home:/.lamin/bionty/sources_local.yaml stores all locally available ontologies.

The content of this file is identical to the public sources.yaml for a freshly-installed Bionty.

Users may edit this file in order to configure customized sources.

Display sources

The available and currently active ontologies can also be printed with bionty.display_available_sources() or bionty.display_currently_used_sources().

Format of the sources yaml file

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"
        md5: "md5 of the source file"

Setting default ontologies and versions

For each entity, the first source and its maximum version in sources_local.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
        md5: 2b7d479d4bd02a94eab47d1c9e64c5db
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
        md5: 04b808d05c2c2e81430b20a0e87552bb
    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
        md5: 9f0c92ad2896dda82195e9226a06dc36
    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
        md5: md5 if available or leave out this row
    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:

Note: changing the order of versions won’t have an effect, as most recent version is taken as default.

Disease:
  mondo:
    all:
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
        md5: 04b808d05c2c2e81430b20a0e87552bb
      2023-02-06:
        source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl
        md5: 2b7d479d4bd02a94eab47d1c9e64c5db
    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
        md5: md5 if available or leave out this row
    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
        md5: 9f0c92ad2896dda82195e9226a06dc36
    name: Human Disease Ontology
    website: https://disease-ontology.org/