Add negative evidence graph guard

knowledge-graph-negative-evidence-guard/package.json

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+{
+  "name": "knowledge-graph-negative-evidence-guard",
+  "version": "1.0.0",
+  "description": "Negative-evidence publication guard for SCIBASE scientific knowledge graph recommendations.",
+  "type": "module",
+  "private": true,
+  "scripts": {
+    "check": "node --check src/index.js && node --check test/index.test.js && node --check scripts/demo.js",
+    "test": "node --test test/index.test.js",
+    "demo": "node scripts/demo.js"
+  },
+  "keywords": [
+    "scibase",
+    "knowledge-graph",
+    "negative-evidence",
+    "retractions",
+    "replication"
+  ],
+  "license": "MIT"
+}

knowledge-graph-negative-evidence-guard/readme.md

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+# Knowledge Graph Negative-Evidence Guard
+
+This module is a focused SCIBASE.AI issue #17 submission for Scientific Knowledge Graph Integration.
+
+It prevents public graph recommendations from quietly routing around negative scientific evidence. The guard inspects synthetic knowledge-graph packets for contradictions, retractions, failed replications, stale unresolved review windows, and private or embargoed negative evidence before entity pages or recommendation edges publish.
+
+## What It Covers
+
+- Retractions or withdrawn evidence blocking dependent graph paths.
+- Conflicting positive and negative evidence requiring curator review.
+- High-confidence failed replications downgrading recommendations until resolved.
+- Public recommendations refusing private or embargoed evidence chains.
+- Reviewer packets that explain blockers, required actions, and recommendation decisions.
+
+## What It Does Not Do
+
+- No live research data is read.
+- No external ontology, DOI, storage, payment, or private repository APIs are called.
+- No credentials, personal data, private manuscripts, or private datasets are included.
+- No broad entity-extraction system is reimplemented; this is a safety gate for negative evidence and recommendation publication.
+
+## Reviewer Path
+
+```bash
+npm run check
+npm test
+npm run demo
+```
+
+Generated reviewer artifacts:
+
+- `reports/negative-evidence-packet.json`
+- `reports/negative-evidence-report.md`
+- `reports/summary.svg`
+
+## Claim
+
+Use `/claim #17` in the pull request body.

knowledge-graph-negative-evidence-guard/reports/negative-evidence-packet.json

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+{
+  "title": "SCIBASE Scientific Knowledge Graph Negative-Evidence Guard",
+  "issue": "SCIBASE.AI#17",
+  "claim": "/claim #17",
+  "purpose": "Prevent public knowledge graph recommendations from hiding contradictions, retractions, failed replications, or private negative evidence.",
+  "evaluation": {
+    "status": "block_publication",
+    "generatedAt": "2026-06-04T00:00:00.000Z",
+    "graphId": "scibase-kg-negative-evidence-demo",
+    "digest": "b245bc907bb0911addeb552f2bd24ed4c51e6f895cceca6840a3985df1af39ac",
+    "counts": {
+      "claims": 4,
+      "recommendations": 2,
+      "blockers": 5,
+      "warnings": 1,
+      "heldRecommendations": 2
+    },
+    "blockers": [
+      {
+        "code": "retracted_evidence_in_graph_path",
+        "claimId": "claim:retracted-dataset-link",
+        "recommendationIds": [
+          "rec:recommend-protocol-v2"
+        ],
+        "message": "A graph path or recommendation still depends on retracted evidence."
+      },
+      {
+        "code": "stale_negative_evidence_review",
+        "claimId": "claim:embargoed-contradiction",
+        "ageDays": 64,
+        "message": "Negative evidence has been unresolved past the stale-review window."
+      },
+      {
+        "code": "private_evidence_used_publicly",
+        "claimId": "claim:embargoed-contradiction",
+        "recommendationIds": [
+          "rec:recommend-gene-x-dataset"
+        ],
+        "message": "A public recommendation uses private or embargoed negative-evidence context."
+      },
+      {
+        "code": "unresolved_contradictory_claims",
+        "tripleKey": "paper:crispr-neuro-2024|supports|finding:gene-x-effect",
+        "conflictScore": 0.644,
+        "positiveClaimIds": [
+          "claim:supports-gene-x"
+        ],
+        "negativeClaimIds": [
+          "claim:failed-replication-gene-x"
+        ],
+        "recommendationIds": [
+          "rec:recommend-gene-x-dataset"
+        ],
+        "message": "Conflicting positive and negative evidence requires curator review before recommendations publish."
+      },
+      {
+        "code": "failed_replication_without_curator_outcome",
+        "claimId": "claim:failed-replication-gene-x",
+        "recommendationIds": [
+          "rec:recommend-gene-x-dataset"
+        ],
+        "message": "High-confidence failed replication evidence needs a curator outcome before graph boosts continue."
+      }
+    ],
+    "warnings": [
+      {
+        "code": "missing_negative_evidence_doi",
+        "claimId": "claim:embargoed-contradiction",
+        "message": "Negative evidence should keep a DOI or stable public source identifier before curator review."
+      }
+    ],
+    "actions": [
+      {
+        "type": "request_curator_decision",
+        "claimId": "claim:embargoed-contradiction",
+        "reason": "Negative evidence is stale and still affects graph recommendations."
+      },
+      {
+        "type": "open_conflict_review",
+        "tripleKey": "paper:crispr-neuro-2024|supports|finding:gene-x-effect",
+        "claimIds": [
+          "claim:supports-gene-x",
+          "claim:failed-replication-gene-x"
+        ],
+        "reason": "Positive and negative evidence both exceed the publication hold threshold."
+      }
+    ],
+    "claimActions": [
+      {
+        "claimId": "claim:retracted-dataset-link",
+        "decision": "block",
+        "reason": "Retracted or withdrawn evidence cannot support public graph recommendations."
+      }
+    ],
+    "recommendationActions": [
+      {
+        "recommendationId": "rec:recommend-gene-x-dataset",
+        "decision": "hold",
+        "reasons": [
+          "private_evidence_for_public_recommendation",
+          "unresolved_conflict",
+          "failed_replication"
+        ],
+        "requiredActions": [
+          "Replace private evidence with a public citation or keep the recommendation internal.",
+          "Redact any embargoed evidence from the public graph packet.",
+          "Attach a curator decision that accepts, qualifies, or suppresses the conflict.",
+          "Show contradiction context on the entity page before publication.",
+          "Downgrade recommendation confidence until the failed replication is resolved.",
+          "Expose failed-replication context beside the graph edge."
+        ]
+      },
+      {
+        "recommendationId": "rec:recommend-protocol-v2",
+        "decision": "hold",
+        "reasons": [
+          "retracted_evidence"
+        ],
+        "requiredActions": [
+          "Remove the retracted claim from recommendation evidence.",
+          "Add a public curator note explaining the withdrawal."
+        ]
+      }
+    ],
+    "policy": {
+      "contradictionHoldConfidence": 0.58,
+      "failedReplicationHoldConfidence": 0.55,
+      "staleReviewDays": 30,
+      "requirePublicEvidenceForPublicRecommendations": true,
+      "retractionsBlockAllRecommendations": true,
+      "requireCuratorForConflicts": true
+    }
+  },
+  "reviewerChecklist": [
+    "Every public recommendation has an explicit evidence chain.",
+    "Retracted evidence blocks dependent graph paths.",
+    "Contradictory evidence opens a curator review before publication.",
+    "Failed replication evidence downgrades recommendations until resolved.",
+    "Private or embargoed evidence is not leaked into public recommendation paths."
+  ]
+}

knowledge-graph-negative-evidence-guard/reports/negative-evidence-report.md

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+# Negative-Evidence Graph Guard Report
+
+Issue: SCIBASE.AI#17
+Claim marker: `/claim #17`
+Status: `block_publication`
+Digest: `b245bc907bb0911addeb552f2bd24ed4c51e6f895cceca6840a3985df1af39ac`
+
+## Reviewer Checklist
+- Every public recommendation has an explicit evidence chain.
+- Retracted evidence blocks dependent graph paths.
+- Contradictory evidence opens a curator review before publication.
+- Failed replication evidence downgrades recommendations until resolved.
+- Private or embargoed evidence is not leaked into public recommendation paths.
+
+## Counts
+- Claims inspected: 4
+- Recommendations inspected: 2
+- Blockers: 5
+- Warnings: 1
+- Held recommendations: 2
+
+## Blockers
+- retracted_evidence_in_graph_path: A graph path or recommendation still depends on retracted evidence.
+- stale_negative_evidence_review: Negative evidence has been unresolved past the stale-review window.
+- private_evidence_used_publicly: A public recommendation uses private or embargoed negative-evidence context.
+- unresolved_contradictory_claims: Conflicting positive and negative evidence requires curator review before recommendations publish.
+- failed_replication_without_curator_outcome: High-confidence failed replication evidence needs a curator outcome before graph boosts continue.
+
+## Warnings
+- missing_negative_evidence_doi: Negative evidence should keep a DOI or stable public source identifier before curator review.
+
+## Recommendation Actions
+- rec:recommend-gene-x-dataset: hold (private_evidence_for_public_recommendation, unresolved_conflict, failed_replication)
+- rec:recommend-protocol-v2: hold (retracted_evidence)
+
+## Required Actions
+- request_curator_decision: Negative evidence is stale and still affects graph recommendations.
+- open_conflict_review: Positive and negative evidence both exceed the publication hold threshold.

knowledge-graph-negative-evidence-guard/scripts/demo.js

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+import fs from "node:fs";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+
+import {
+  buildReviewerPacket,
+  demoPacket,
+  renderMarkdownReport,
+  renderSvgSummary
+} from "../src/index.js";
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+const moduleRoot = path.resolve(__dirname, "..");
+const reportsDir = path.join(moduleRoot, "reports");
+const now = "2026-06-04T00:00:00.000Z";
+const packet = demoPacket();
+const reviewerPacket = buildReviewerPacket(packet, { now });
+
+fs.mkdirSync(reportsDir, { recursive: true });
+fs.writeFileSync(path.join(reportsDir, "negative-evidence-packet.json"), `${JSON.stringify(reviewerPacket, null, 2)}\n`);
+fs.writeFileSync(path.join(reportsDir, "negative-evidence-report.md"), renderMarkdownReport(packet, { now }));
+fs.writeFileSync(path.join(reportsDir, "summary.svg"), renderSvgSummary(packet, { now }));
+
+console.log(JSON.stringify({
+  status: reviewerPacket.evaluation.status,
+  digest: reviewerPacket.evaluation.digest,
+  blockers: reviewerPacket.evaluation.counts.blockers,
+  warnings: reviewerPacket.evaluation.counts.warnings,
+  reportsDir
+}, null, 2));