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Phenotype scrambling utilities

This page documents utilities used to introduce noise or perturbations into phenotype data. These commands are typically used to assess the robustness and sensitivity of phenotype-driven prioritisation methods.

They operate on existing phenotype data and do not execute tools or perform benchmarking directly.

Purpose

Phenotype scrambling utilities are used to:

  • Simulate noisy or incomplete phenotypic observations
  • Evaluate how sensitive methods are to phenotype quality
  • Test robustness under controlled perturbations

These experiments are useful when comparing tools, parameterisations, or ontology versions.

Scrambling phenopackets

The scramble-phenopackets command generates perturbed versions of existing phenopackets.

The scrambled phenopackets can then be used as inputs to runners for execution and benchmarking.

Example: scramble a phenopacket corpus

Generate scrambled phenopackets from an existing corpus:

pheval-utils scramble-phenopackets \
  --phenopacket-dir phenopackets/ \
  --output-dir scrambled_phenopackets/ \
  --scramble-factor 0.7 \
  --local-ontology-cache ./hp.obo

Notes:

  • The original phenopackets are not modified.
  • Scrambled outputs are written to a separate directory.
  • The resulting phenopackets can be used directly with plugin-provided runners.

How phenotype scrambling fits into a workflow

A typical robustness experiment using phenotype scrambling might look like:

  1. Prepare a clean phenopacket corpus
  2. Generate scrambled phenopackets
  3. Run tools via plugin-provided runners using pheval run
  4. Benchmark and compare performance against the original results

Scrambling utilities are optional and primarily used in experimental or methodological evaluations.