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PTM Benchmark Lineage

The ptm family now has a two-root lineage instead of one convenient package story. This page ties the primary flagship package, the companion generalization package, and the cross-package drift report together so an outsider can follow the evidence chain from copied input to derived review surface.

Family Contract

  • benchmark title: PTM localization public benchmark package
  • public dataset identity: tracked localization, PTM feature, raw-spectrum, and sequence-context snapshots with explicit ambiguity limits
  • dataset locator: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json
  • evidence tier: external_reproduction_package
  • primary package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package
  • companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package
  • cross-package generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json

Raw Source Trail

primary flagship package

  • PTM localization result snapshot copies packages/bijux-proteomics-core/tests/fixtures/ptm/localization_results.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/localization_results.tsv
  • checksum: a711e01b793af64df1c24802a661a53eb8c88a7d5abee2b66cd7fab89cc054d1
  • public reference: https://pubmed.ncbi.nlm.nih.gov/16964243/
  • rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh

companion generalization package

  • PTM ambiguity-stress localization snapshot copies packages/bijux-proteomics-core/tests/fixtures/ptm/localization_results.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/evidence/localization_results.tsv
  • checksum: f85243b0a4a3332e52671a60ce6f397202d9aa7ec1f15a6abf57a436a55d2150
  • public reference: https://github.com/bijux/bijux-proteomics
  • rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh

Derived Review Surfaces

  • primary package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json
  • primary artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/artifact_inventory.json
  • primary quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/quality_sheet.json
  • companion package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/package_manifest.json
  • companion artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/artifact_inventory.json
  • companion quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/quality_sheet.json
  • family drift report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json

What This Lineage Does And Does Not Prove

  • primary claim scope: Flagship public PTM localization review package keeps ptm review grounded in packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package rather than abstract benchmark prose.
  • companion claim scope: Companion public PTM ambiguity-stress review package exists to show where ptm family transfer weakens, not to hide that drift.
  • current cross-package note: This report is the public family-transfer surface. It records what still survives when the workflow moves from the flagship primary package to a second package with a materially different pressure profile.

Rebuild Order

  1. Refresh the primary root with uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh.
  2. Refresh the companion root with uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh.
  3. Re-read the family drift report before strengthening any workflow-family sentence.