Configuration

OptimusKG separates code from settings using Kedro's configuration system. All configuration lives in the conf/ directory.

Directory Structure

conf/
  base/                    # Shared configuration (committed to git)
    catalog/               # Dataset definitions by layer and source
      landing/
      bronze/
      silver/
    parameters.yml         # Runtime parameters
    biocypher/             # BioCypher schema and export config
      schema_config.yaml   # Node and edge type definitions
    logging.yml            # Logging configuration
  local/                   # Local overrides (gitignored)

Environments

• base: Default configuration shared across all environments. Always loaded first.
• local: Machine-specific overrides. Gitignored for credentials and local paths.

Kedro merges local over base, so local settings take precedence.

Parameters

conf/base/parameters.yml defines runtime constants used across pipelines:

gold:
  export_formats:
    csv:
      properties: true
    parquet:
      properties: true

Parameters are injected into nodes via Kedro's dependency injection using params: prefixed inputs.

BioCypher Configuration

conf/base/biocypher/schema_config.yaml defines the knowledge graph schema:

• Node types: Gene, Drug, Disease, Protein, Anatomy, Pathway, Phenotype, Exposure, Biological Process, Cellular Component, Molecular Function
• Edge types: All relationship types between node types
• Properties: Attributes for each node and edge type

This schema drives the gold layer export via BioCypher.