chore: mark Q5 complete + add Phase R to NEXT_100_PR_MAP

docs/research/NEXT_100_PR_MAP.md

@@ -210,4 +210,16 @@ Close the loop between dry-lab nominations and actual experimental outcomes. Fir
 | Q2 | Add wet-lab hit record schema (WHR-) (complete). — src/openamp_foundry/evidence/wetlab_hit_record.py: WHR- 16-field schema; dry_lab_only=False enforced; VALID_EXPERIMENT_TYPES (10), VALID_INTERPRETATIONS (active/inactive/inconclusive), proof_ladder_level cap; 59 tests in tests/evidence/test_wetlab_hit_record.py. | First machine-readable record of actual experimental outcome; dry_lab_only must be False; closes nomination→experiment loop. | B/C |
 | Q3 | Add post-experiment calibration update schema (complete). — src/openamp_foundry/evidence/post_experiment_calibration_update.py: PCU- 16-field schema; dry_lab_only=False enforced; human_reviewed=True required; VALID_UPDATE_DIRECTIONS (5), VALID_CALIBRATION_TRIGGER_TYPES (7); n_whr_records/whr_ids consistency check; 55 tests in tests/evidence/test_post_experiment_calibration_update.py. | Records how wet-lab results change score calibration; evidence trail for model improvement decisions. | B/C |
 | Q4 | Add hit confirmation report generator (complete). — src/openamp_foundry/evidence/hit_confirmation_report.py: HCR- 16-field schema; VALID_CONFIRMATION_VERDICTS (4), VALID_DIVERGENCE_TYPES (7), VALID_PREDICTION_QUALITY_GRADES (A/B/C/D/N/A); dry_lab_only=False enforced; confirmed_hit requires n_confirmed≥1; not_confirmed requires n_inactive≥1; no_divergence exclusive with other divergence types; 70 tests in tests/evidence/test_hit_confirmation_report.py. | Bundles WHR- records with pre-registration for reproducibility check; flags prediction vs actual divergence. | B/C |
-| Q5 | Add Phase Q completeness gate (closes Phase Q). | Machine-verifiable that the full dry-lab→wet-lab→calibration loop has run for at least one candidate family. | C |
+| Q5 | Add Phase Q completeness gate (closes Phase Q) (complete). — src/openamp_foundry/evidence/phase_q_completeness_gate.py: PQG- 12-field schema; REQUIRED_RECORD_TYPES (BSP/WHR/PCU/HCR), VALID_LOOP_VERDICTS (4); loop_complete enforces all four record types and no cross-link failures; dry_lab_only=False enforced; n_candidates_with_hcr ≤ n_candidates_with_whr enforced; 68 tests in tests/evidence/test_phase_q_completeness_gate.py. | Machine-verifiable that the full dry-lab→wet-lab→calibration loop has run for at least one candidate family. | C |
+
+## Phase R — Scientific output readiness
+
+Make the full pipeline auditable and reviewable by external scientists. First phase where the system produces outputs that could accompany a preprint or data release.
+
+| PR | Task | Why it matters | Review class |
+|---:|---|---|---|
+| R1 | Add candidate family clustering evidence schema (CFC-). | Machine-verifiable grouping of related candidates into a "novel family" claim; sequence similarity threshold, family size, novelty evidence type controlled vocabulary. | B/C |
+| R2 | Add family novelty report schema (FNR-). | Bundles CFC- clustering with cheap-baseline comparison; prevents "novel family" overclaim when candidates are merely sequence variants of known AMPs. | B/C |
+| R3 | Add full audit trail report schema (ATR-) linking BSP→WHR→PCU→HCR→PQG for a complete dry-lab→wet-lab loop trace. | End-to-end chain of custody from nomination to confirmed hit; required for scientific reproducibility. | B/C |
+| R4 | Add scientific review readiness gate schema (SRG-). | Machine-verifiable checklist for when a candidate family has enough evidence for external scientific review; requires CFC+FNR+ATR+PQG records and no unresolved safety flags. | C |
+| R5 | Add preprint evidence bundle schema (PEB-) — read-only snapshot of all evidence for a run. | External reviewers can verify every claim from a single self-contained artifact; closes Phase R. | C |