Providers

Providers handle automatic, versioned data downloads from external sources. They are used by the Origin Hook and defined in optimuskg/hooks/origin/providers/.

How Providers Work

Each catalog entry can specify a metadata.origin field that configures which provider to use and how to download the data:

landing.opentargets.disease:
  type: optimuskg.datasets.polars.ParquetDataset
  filepath: data/landing/opentargets/disease.parquet
  metadata:
    origin:
      provider: opentargets
      dataset: diseases

When the Origin Hook detects a missing file, it delegates the download to the configured provider.

Available Providers

HTTP Provider

File: optimuskg/hooks/origin/providers/http.py

Downloads files from HTTP/HTTPS URLs. The simplest provider for publicly available data.

OpenTargets Provider

File: optimuskg/hooks/origin/providers/opentargets.py

Downloads data from the Open Targets Platform API. Handles the platform's specific data distribution format.

BioOntology Provider

File: optimuskg/hooks/origin/providers/bioontology.py

Downloads ontology files from the BioPortal/BioOntology API. Used for ontologies like GO, HP, MONDO, and UBERON.

DrugBank Provider

File: optimuskg/hooks/origin/providers/drugbank.py

Downloads data from DrugBank. Requires authentication credentials for access to the full dataset.