From 5a7f790720a72a7a5ec3b3f8cb85dcb774356010 Mon Sep 17 00:00:00 2001 From: OpenCode Date: Fri, 10 Jul 2026 13:49:57 +0700 Subject: [PATCH] chore: mark R2 complete in NEXT_100_PR_MAP (#958) --- docs/research/NEXT_100_PR_MAP.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/research/NEXT_100_PR_MAP.md b/docs/research/NEXT_100_PR_MAP.md index 8560eb70..b08d5c74 100644 --- a/docs/research/NEXT_100_PR_MAP.md +++ b/docs/research/NEXT_100_PR_MAP.md @@ -219,7 +219,7 @@ Make the full pipeline auditable and reviewable by external scientists. First ph | PR | Task | Why it matters | Review class | |---:|---|---|---| | R1 | Add candidate family clustering evidence schema (CFC-) (complete). — src/openamp_foundry/evidence/candidate_family_clustering.py: CFC- 15-field schema; VALID_NOVELTY_EVIDENCE_TYPES (6), VALID_CLUSTERING_METHODS (5), VALID_NOVELTY_VERDICTS (4); novel_family requires hard evidence (blast/hmm/structural/charge); variant_of_known requires known_family_hits; n_candidates≥2 enforced; dry_lab_only=True enforced; 66 tests in tests/evidence/test_candidate_family_clustering.py. | 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 | +| R2 | Add family novelty report schema (FNR-) (complete). — src/openamp_foundry/evidence/family_novelty_report.py: FNR- 13-field schema; VALID_BASELINE_COMPARISON_OUTCOMES (4), VALID_NOVELTY_STRENGTH_GRADES (4), VALID_CHEAP_BASELINES_CHECKED (5); strong grade requires outside_known_space; not_supported incompatible with outside_known_space; cheap_enemy_score/family_score in [0,1]; dry_lab_only=True enforced; 64 tests in tests/evidence/test_family_novelty_report.py. | 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 |