feat: Phase M M2 claim-to-evidence mapper schema -- maps scientific claims to supporting artifacts for external audit

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check dataset-release-check
+.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check claim-to-evidence-check dataset-release-check
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -936,6 +936,9 @@ pipeline-decision-audit-check:
 		--entry-json '{"audit_id":"AUD-001","batch_id":"BATCH-001","pipeline_version":"0.8.9","decision_date":"2026-07-09","decision_type":"filter_applied","decision_description":"Applied hemolysis fraction filter at threshold 0.15.","rationale":"Threshold pre-specified in BENCHMARK_GOVERNANCE.md based on Wave 0 data.","alternatives_considered":["threshold 0.10","threshold 0.20"],"affected_candidate_count":47,"evidence_level":4,"pre_specified":true,"reviewer":"alice","dry_lab_only":true}' \
 		--format text
 
+claim-to-evidence-check:
+	.venv/bin/openamp-foundry claim-to-evidence-check --entry-json '{"mapping_id":"CEM-001","batch_id":"BATCH-001","pipeline_version":"0.9.0","claim_text":"Test claim","claim_type":"activity_prediction","supporting_artifact_ids":["CERT-001","SEL-001"],"evidence_level":3,"pre_specified":true,"reviewer":"test@example.com","dry_lab_only":true}' --format text
+
 dataset-release-check:
 	.venv/bin/openamp-foundry dataset-release-check \
 		--entry-json '{"release_id":"DSR-001","dataset_name":"OpenAMP Wave 0.5 Candidates","dataset_version":"1.0.0","release_date":"2026-07-09","license_identifier":"CC-BY-4.0","data_sources":["UniProt AMP database","APD3","in-house pipeline"],"contains_sequences":true,"contains_activity_data":false,"dual_use_assessed":true,"usage_policy_url":"https://openamp.example.org/data-policy","contact_email":"data@openamp.example.org","release_approved":true,"dry_lab_only":true}' \

docs/evidence/CLAIM_TO_EVIDENCE_GUIDE.md

@@ -0,0 +1,62 @@
+# Claim-to-Evidence Mapper Guide
+
+## Purpose
+
+The claim-to-evidence mapper records which artifacts support each scientific
+claim made by the pipeline. Every claim must trace to at least one artifact.
+External auditors use this map to verify that claims are not free-floating.
+
+## Schema Fields
+
+| Field | Type | Description |
+|---|---|---|
+| mapping_id | str | Unique identifier (prefix "CEM-") |
+| batch_id | str | Batch this mapping belongs to |
+| pipeline_version | str | Pipeline version string |
+| claim_text | str | The claim being made (max 500 chars) |
+| claim_type | str | Category of claim (see valid types) |
+| supporting_artifact_ids | list[str] | IDs of artifacts that support this claim |
+| evidence_level | int | 1–6 evidence hierarchy level |
+| pre_specified | bool | True if claim was pre-specified before analysis |
+| reviewer | str | Reviewer who validated this mapping |
+| dry_lab_only | bool | Always True for computational claims |
+
+## Valid Claim Types
+
+- `activity_prediction` — predicted antimicrobial activity
+- `calibration_statement` — statements about model calibration
+- `novelty_claim` — claim about sequence novelty vs. known AMPs
+- `performance_comparison` — comparison against a baseline or benchmark
+- `reproducibility_claim` — claim that results can be reproduced
+- `safety_assessment` — claims about toxicity/hemolysis/dual-use risk
+- `selection_rationale` — rationale for selecting a candidate
+
+## Validation Rules
+
+1. mapping_id must start with "CEM-"
+2. claim_text must not be empty and must not exceed 500 characters
+3. claim_type must be one of the valid types listed above
+4. supporting_artifact_ids must contain at least 1 artifact ID
+5. evidence_level must be between 1 and 6
+6. reviewer must not be empty
+7. dry_lab_only must be True (computational claims only)
+
+## Warning Conditions
+
+- Post-hoc claim: pre_specified=False → warn that claim may be exploratory
+- Weak evidence: evidence_level <= 2 → warn that evidence is limited
+- Single artifact: exactly 1 supporting artifact → warn to seek corroboration
+- Long claim text: claim_text > 300 chars → warn for conciseness
+
+## Honest Use Boundary
+
+A claim-to-evidence mapping records the *computational* support for a claim.
+It does not imply biological validity. Claims mapped here are dry-lab outputs
+only. Do not use this schema to record claims from wet-lab experiments.
+
+## CLI Usage
+
+```bash
+openamp-foundry claim-to-evidence-check --entry-json '{"mapping_id": "CEM-001", ...}' --format text
+openamp-foundry claim-to-evidence-check --entry-json '{"mapping_id": "CEM-001", ...}' --format json
+```

docs/evidence/METRICS_CURRENT.md

@@ -5,7 +5,8 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **Purpose:** One authoritative table of current pipeline metrics. If any doc disagrees
 > with this file, this file wins. Updated whenever benchmark/benchmark config changes.
 >
-> **Last updated:** 2026-07-09 (Phase M M1 — pipeline decision audit entry schema — v0.8.9)
+> **Last updated:** 2026-07-09 (Phase M M2 — claim-to-evidence mapper schema — v0.9.0)
+> **New in v0.9.0:** Claim-to-evidence mapper schema (M2 — Loop 129) — docs/evidence/CLAIM_TO_EVIDENCE_GUIDE.md with purpose, schema fields table (10 fields), valid claim types (7), validation rules (7), warning conditions (4), honest-use boundary, CLI usage. src/openamp_foundry/evidence/claim_to_evidence_mapper.py with ClaimToEvidenceEntry dataclass (10 fields: mapping_id, batch_id, pipeline_version, claim_text, claim_type, supporting_artifact_ids, evidence_level, pre_specified, reviewer, dry_lab_only=True), ClaimToEvidenceResult dataclass (7 fields: mapping_id, batch_id, claim_type, passed, errors, warnings, dry_lab_only=True), VALID_CLAIM_TYPES (7: activity_prediction, calibration_statement, novelty_claim, performance_comparison, reproducibility_claim, safety_assessment, selection_rationale), VALID_EVIDENCE_LEVELS (6: 1-6), MAX_CLAIM_TEXT_LENGTH (500), LONG_CLAIM_TEXT_THRESHOLD (300), WEAK_EVIDENCE_THRESHOLD (2), validate_claim_to_evidence() (7 error checks: CEM- prefix, non-empty claim_text<=500 chars, valid claim_type, non-empty supporting_artifact_ids, valid evidence_level 1-6, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: post-hoc, weak evidence, single artifact, long claim text), validate_claim_to_evidence_dict() (9 required fields guard). CLI (openamp-foundry claim-to-evidence-check) with --entry-json, --format text|json. make claim-to-evidence-check target. Phase M M2: every scientific claim is now machine-mapped to its supporting artifacts for external audit.
 > **New in v0.8.9:** Pipeline decision audit entry schema (M1 — Loop 128) — docs/evidence/PIPELINE_DECISION_AUDIT_GUIDE.md with purpose, required field table (13 fields), valid decision types (7), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/pipeline_decision_audit.py with PipelineDecisionAuditEntry dataclass (13 fields: audit_id, batch_id, pipeline_version, decision_date, decision_type, decision_description, rationale, alternatives_considered, affected_candidate_count, evidence_level, pre_specified, reviewer, dry_lab_only), PipelineDecisionAuditResult dataclass (5 fields: audit_id, batch_id, decision_type, passed, errors, warnings, dry_lab_only=True), VALID_DECISION_TYPES (7: benchmark_updated, calibration_adjusted, candidate_ranked, candidate_rejected, filter_applied, safety_flag_applied, threshold_chosen), VALID_EVIDENCE_LEVELS (6: 1-6), MAX_DESCRIPTION_LENGTH (500), MAX_RATIONALE_LENGTH (1000), validate_pipeline_decision_audit() (12 checks: AUD- prefix, non-empty batch_id/pipeline_version/reviewer, YYYY-MM-DD decision_date, valid decision_type, non-empty description<=500 chars, non-empty rationale<=1000 chars, affected_candidate_count>=0, valid evidence_level, dry_lab_only must be True; post-hoc warns, empty alternatives warns, low evidence warns, zero affected warns), validate_pipeline_decision_audit_dict() (12 required fields guard). CLI (openamp-foundry pipeline-decision-audit-check) with --entry-json, --format text|json. make pipeline-decision-audit-check target. Phase M M1: every pipeline decision is now machine-validated and traceable for external audit.
 > **New in v0.8.8:** Dataset release package checker (L5 — Loop 127) — docs/evidence/DATASET_RELEASE_GUIDE.md with purpose, required field table (13 fields), valid license identifiers (5), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/dataset_release.py with DatasetReleaseEntry dataclass (13 fields: release_id, dataset_name, dataset_version, release_date, license_identifier, data_sources, contains_sequences, contains_activity_data, dual_use_assessed, usage_policy_url, contact_email, release_approved, dry_lab_only), DatasetReleaseResult dataclass (4 fields: release_id, dataset_name, passed, errors, warnings, dry_lab_only=True), VALID_LICENSE_IDENTIFIERS (5: Apache-2.0, CC-BY-4.0, CC-BY-NC-4.0, CC0-1.0, MIT), MINIMUM_DATA_SOURCES (1), validate_dataset_release() (11 checks: DSR- prefix, non-empty dataset_name/dataset_version/usage_policy_url/contact_email, YYYY-MM-DD release_date, valid license_identifier, data_sources>=1, dual_use_assessed must be True, release_approved must be True, dry_lab_only must be True; CC-BY-NC-4.0 warns, single source warns), validate_dataset_release_dict() (12 required fields guard). CLI (openamp-foundry dataset-release-check) with --entry-json, --format text|json. make dataset-release-check target. Phase L L5 completes Phase L: open dataset releases now have machine-validated data governance checks.
 > **New in v0.8.7:** Multi-candidate comparison schema (L4 — Loop 126b) — docs/evidence/MULTI_CANDIDATE_COMPARISON_GUIDE.md with purpose, required field table (11 fields), minimum requirements (2 candidates, 2 criteria), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/multi_candidate_comparison.py with MultiCandidateComparisonEntry dataclass (11 fields: comparison_id, batch_id, pipeline_version, comparison_date, candidate_ids, comparison_criteria, top_candidate_id, top_candidate_rationale, evidence_level, reviewer, dry_lab_only), MultiCandidateComparisonResult dataclass (5 fields: comparison_id, batch_id, candidate_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_CANDIDATES (2), MINIMUM_CRITERIA (2), RECOMMENDED_CRITERIA (3), MAX_RATIONALE_LENGTH (500), LARGE_CANDIDATE_SET_THRESHOLD (10), VALID_EVIDENCE_LEVELS (6: 1-6), validate_multi_candidate_comparison() (11 checks: CMP- prefix, non-empty batch_id/pipeline_version/reviewer, YYYY-MM-DD comparison_date, candidate_ids>=2, comparison_criteria>=2, top_candidate_id in candidate_ids, non-empty rationale<=500 chars, valid evidence_level, dry_lab_only must be True; evidence_level<=2 warns, candidate_count>10 warns, criteria_count<3 warns), validate_multi_candidate_comparison_dict() (10 required fields guard). CLI (openamp-foundry multi-candidate-comparison-check) with --entry-json, --format text|json. make multi-candidate-comparison-check target. Phase L L4: side-by-side candidate comparisons are now machine-validated for publication-ready supplementary tables.

docs/research/NEXT_100_PR_MAP.md

@@ -220,7 +220,7 @@ Make every pipeline decision traceable, independently verifiable, and resistant
 | PR | Task | Why it matters | Review class |
 |---:|---|---|---|
 | M1 | Add pipeline decision audit entry schema (complete — Loop 128). | Records filter/threshold/rank decisions with rationale for external audit. | B |
-| M2 | Add claim-to-evidence mapper schema. | Maps each scientific claim to the artifact that supports it. | B |
+| M2 | Add claim-to-evidence mapper schema (complete — Loop 129). | Maps each scientific claim to the artifact that supports it. | B |
 | M3 | Add score decomposition report schema. | Documents how composite scores are computed from components. | B |
 | M4 | Add reviewer briefing package checker. | One-stop summary that external reviewers need before auditing. | B |
 | M5 | Add audit chain completeness checker. | Validates the evidence chain has no gaps from sequences to submission. | B/D |

docs/research/ROADMAP.md

@@ -1,5 +1,11 @@
 # Roadmap
 
+### v0.9.0 — Phase M M2: Claim-to-Evidence Mapper
+- Added `ClaimToEvidenceEntry` schema mapping each claim to supporting artifacts
+- 7 valid claim types; 4 warning conditions for exploratory or weakly-evidenced claims
+- CLI: `openamp-foundry claim-to-evidence-check`
+- 50 tests; all passing
+
 ### v0.8.9
 - Phase M M1: pipeline decision audit entry schema — records each filter/threshold/rank decision with rationale and alternatives considered for external audit. PipelineDecisionAuditEntry dataclass, validate_pipeline_decision_audit(), CLI pipeline-decision-audit-check.
 

src/openamp_foundry/cli/commands/reports.py

@@ -3192,3 +3192,36 @@ def _run_pipeline_decision_audit_check(args: argparse.Namespace) -> int:
             print("  Pipeline decision audit validated. Decision is traceable and reviewable.")
 
     return 0 if result.passed else 3
+
+
+def _run_claim_to_evidence_check(args: argparse.Namespace) -> int:
+    import json as _json
+    from openamp_foundry.evidence.claim_to_evidence_mapper import validate_claim_to_evidence_dict
+
+    try:
+        d = _json.loads(args.entry_json)
+    except _json.JSONDecodeError as exc:
+        print(_json.dumps({"status": "error", "error": f"Invalid JSON: {exc}"}))
+        return 2
+
+    if not isinstance(d, dict):
+        print(_json.dumps({"status": "error", "error": "--entry-json must be a JSON object"}))
+        return 2
+
+    result = validate_claim_to_evidence_dict(d)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        import dataclasses
+        print(_json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        print(f"[{status}] Claim-to-Evidence Check: {result.mapping_id}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Claim-to-evidence mapping validated. Claim is traceable to supporting artifacts.")
+
+    return 0 if result.passed else 3