Bases: BaseProcessor

Processor for KrishnanLab annotations.

Provides expert-curated tissue and disease annotations for GEO samples. Disease IDs are mapped from DOID to MONDO and filtered to system-level descendants. Tissue UBERON/CL IDs are filtered to system-level descendants.

process(output_dir, **kwargs)

Process KrishnanLab TSV into standardized sample annotations.

Parameters:
  • output_dir (Path) –

    Directory where the processed parquet file will be written.

  • **kwargs (Any, default: {} ) –

    input_path (Path | str) — override the default input path (defaults to KRISHNANLAB_TSV from config).
Returns:
  • DataFrame –

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

validate(data)

Validate processed KrishnanLab data.

Parameters:
  • data (DataFrame) –

    Processed annotations DataFrame to validate.
Returns:
  • bool –

    True if validation passes.
Raises: