Bases: BaseProcessor

Processor for CREEDS crowd-sourced disease annotations.

CREEDS provides crowd-sourced annotations for disease perturbations with both control and perturbation sample annotations.

process(output_dir, **kwargs)

Process CREEDS annotations into standardized format.

Parameters:
  • output_dir (Path) –

    Directory where the processed parquet file will be written.

  • **kwargs (Any, default: {} ) –

    input_path (Path) - override CREEDS JSON input file
Returns:
  • DataFrame –

    Standardized annotations with columns sample_id, annotation_type, term_id, term_label, and ecode.

validate(data)

Validate processed CREEDS data.

Parameters:
  • data (DataFrame) –

    Processed annotations DataFrame to validate.
Returns:
  • bool –

    True if validation passes.
Raises: