genome-validate

name

genome-validate

description

Multi-agent validation pipeline for fact-checking claims, verifying evidence tiers, and ensuring prescriber document accuracy. Uses Codex CLI, NotebookLM, PubMed subagents, and Tavily search. Supports: audit (full vault), gene SYMBOL (single gene fact-check), protocol NAME (protocol/report fact-check). Triggers on: /genome-validate, "validate this note", "fact-check", "cross-check claims", "verify evidence", "audit this report", "fact-check gene X", "check protocol X".

Genome Validate

Multi-agent validation for genome vault claims and reports.

Vault Configuration

• Agent config: config/agents.yaml
• Validation logic: scripts/lib/multi_agent.py
• Evidence tiers: config/evidence_tiers.yaml

Validation Modes

Mode 1: Single Note Validation

Validate a specific gene note or research finding.

1. Read the note content
2. Dispatch to configured agents in parallel:
   • Codex CLI: Review evidence tiers, effect sizes, drug interactions
   • Claude subagent (PubMed): Search for recent publications on this gene
   • Tavily: Check for retractions of cited papers
3. Aggregate results using consensus logic
4. Report: pass/warn/block with specific flags

Gate: gene_note — requires 1 agent pass, blocks on effect_size_mismatch, wrong_evidence_tier

Mode 2: Report Validation (Gated)

Validate prescriber-facing documents (Wallet Card, PGx Card, Prescriber Summary).

1. Read the report content
2. Dispatch to agents:
   • Codex CLI: Check drug contraindications against CPIC guidelines
   • NotebookLM: Verify claims against uploaded source papers
   • Claude subagent: Cross-reference drug interactions
3. Apply strict consensus gate
4. BLOCK publication if safety-critical errors found

Gate: prescriber_report — requires 2 agents agree, zero tolerance on drug safety

Mode 3: Full Vault Audit

Comprehensive multi-agent audit of the entire vault.

1. Run Python audit scripts (graph, consistency, staleness, evidence, claims)
2. Dispatch to agents:
   • Codex CLI: Review top 10 highest-PageRank notes
   • NotebookLM: Check prescriber docs vs research notes for contradictions
   • Tavily: Scan for retractions and safety alerts
   • Claude subagent: PubMed scan for new publications
3. Generate unified audit report

Gate: vault_audit — advisory only, no blocking

Agent Integration

Codex CLI

echo "PROMPT" | codex exec --skip-git-repo-check -m gpt-5-codex --config model_reasoning_effort="high" --sandbox read-only --full-auto -C $GENOME_VAULT_ROOT 2>/dev/null

NotebookLM

Use the notebooklm skill to upload source papers and query. Requires manual source upload for new validations.

PubMed Subagent

Launch Claude Explore agent with PubMed search focus.

Tavily

Use the tavily-search skill for web-based verification.

Consensus Logic

From config/agents.yaml:

• effect_size_tolerance: 20% — flag if agents disagree by more
• evidence_tier_tolerance: 1 tier — flag if agents disagree by more
• drug_interaction_strict: true — zero tolerance on safety claims
• require_human_for_blocks: true — human must override blocks

Mode 4: Single Gene Fact-Check

Fact-check a single gene note against primary data and literature.

/genome-validate gene COMT

Steps

1. Verify genotypes vs SQLite
   • Query data/genome.db for all variants in the gene note
   • Compare stated genotypes, rsIDs, and allele calls against database
   • Flag mismatches, missing variants, or stale r2_quality values
2. Check clinical claims via web search
   • Use Tavily to verify effect sizes, drug interaction claims, phenotype associations
   • Cross-reference CPIC/DPWG guidelines for pharmacogenes
   • Flag retracted or superseded studies
3. Validate evidence tiers
   • Compare assigned tiers (E1-E5) against current literature strength
   • Flag tier inflation (e.g., E2 claim supported by single study)
   • Check gene-gene interaction claims for formal testing evidence
4. Identify gaps
   • Missing "What Changes This" section
   • Missing drug interactions for known pharmacogenes
   • Absent cross-references to existing vault genes/systems

Output: Per-claim validation with pass/warn/flag status and suggested corrections.

Mode 5: Protocol/Report Fact-Check

Fact-check a protocol, report, or phenotype note.

/genome-validate protocol "Sertraline Optimization"
/genome-validate report "Prescriber Summary"

Steps

1. Verify gene-recommendation links
   • For each recommendation, confirm the referenced gene note exists and genotype supports the claim
   • Check that cited evidence tiers match the source gene notes
   • Flag recommendations that reference genes not in the vault
2. Supplement safety check
   • Cross-reference supplements against current medications (from vault context)
   • Use Tavily to check for recent safety alerts or contraindication updates
   • Flag drug-supplement and supplement-supplement interactions
3. Evidence tier validation
   • Verify protocol-level evidence tier is not higher than its weakest supporting gene claim
   • Flag speculative recommendations (E4-E5) presented without caveats
4. Completeness check
   • Monitoring schedule present and realistic
   • Dosage ranges match published guidelines
   • Missing contraindications or precautions

Gate: prescriber_report gate applies if the note is in Reports/. Protocol notes use advisory mode (no blocking).

Output

• Validation report (markdown) with per-agent results
• Pass/warn/block status
• Specific flags with suggestions for correction
• Recommendations for follow-up