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DDA Cross-Package Handbook

DDA shows how one workflow claim crosses all six canonical product owners without becoming ownerless. The current lane is scientifically substantive and reviewable, but its Runtime mode remains import_only: repository execution begins from tracked external-engine exports rather than raw-search execution.

flowchart LR
    F["Foundation contracts"] --> C["Core DDA normalization and benchmark"]
    C --> R["Runtime import_only lane"]
    R --> K["Knowledge grounding and contradiction"]
    K --> I["Intelligence judgment or refusal"]
    I --> L["Lab feasibility and consequence"]
    L --> Q{"bounded public claim"}

Owner Chain

Owner DDA responsibility Evidence to inspect
bijux-proteomics-foundation identifiers, document envelopes, canonical JSON, hashes serialized artifact metadata and content identity
bijux-proteomics-core search-export adapters, target-decoy semantics, protein rollup caution, benchmark packages DDA benchmark lineage and acceptance bars
bijux-proteomics-runtime declared input boundary, bundle, lineage, replay, refusal black-box dashboard and execution boundary
bijux-proteomics-knowledge citations, comparator context, claim support, contradictions claim grounding and literature audit
bijux-proteomics-intelligence confidence, downgrade triggers, recommendation, refusal recommendation challenges and decision brief
bijux-proteomics-lab follow-up feasibility, controls, burden, observed outcome consequence map and outcome learning loop

Evidence Flow

  1. Core reads tracked MaxQuant and comparator exports while retaining engine, field-loss, target-decoy, and protein-inference limits.
  2. Runtime reopens that declared package and emits a checked bundle, stage lineage, and failure replay. It does not execute the external search engine.
  3. Knowledge connects the normalized result to source, comparator, literature, and contradiction records.
  4. Intelligence applies an explicit bounded policy and may downgrade or refuse the requested public sentence.
  5. Lab evaluates whether follow-up controls, capacity, burden, and outcome evidence justify action.

No downstream layer repairs an upstream evidence gap. A reproducible import does not become raw-search parity; grounding does not become recommendation; and recommendation does not become laboratory readiness.

Claim Ceiling

The DDA lane can support review of adapter-normalized evidence and its retained limitations. It cannot currently support vendor-native or engine-native raw reproducibility, unbounded cross-engine equivalence, or automatic laboratory consequence. The public sentence must follow the narrower black-box result when the requested outsider_auditable_bounded posture exceeds the dashboard's review_grade_bounded result.

Challenge Route