Directory Generate 3lens

Three-Lens Directory Generator

Generate comprehensive, clinically rigorous directory entries for the NGM Commons platform using a structured three-lens analytical framework.

Invocation

/directory-generate-3lens <product_name> [options]

Arguments:

• <product_name> - Product to analyze (e.g., "Metformin", "Pendulum Glucose Control")
• --output-dir PATH - Custom output directory (default: content/commons/)
• --resume - Resume from last checkpoint if interrupted
• --dry-run - Show execution plan without running
• --rerun-lens L1|L2|L3 - Force re-run specific lens

Three-Lens Framework

This skill applies three distinct analytical lenses, executed in parallel where possible:

┌─────────────────────────────────────────────────────────────────────┐
│                      PARALLEL LENS EXECUTION                         │
│                                                                      │
│  ┌──────────────────┐  ┌──────────────────┐  ┌──────────────────┐  │
│  │     LENS 1       │  │     LENS 2       │  │     LENS 3       │  │
│  │   Mechanistic    │  │   Literature     │  │   KB Cross-Ref   │  │
│  │                  │  │                  │  │                  │  │
│  │ Claude Opus 4.5  │  │ Perplexity Deep  │  │ Local JSON       │  │
│  │ via OpenRouter   │  │ via OpenRouter   │  │ (no LLM)         │  │
│  └────────┬─────────┘  └────────┬─────────┘  └────────┬─────────┘  │
│           │                     │                     │            │
│           ▼                     ▼                     ▼            │
│      Quality Gate          Quality Gate          Quality Gate      │
│      (iterate)             (iterate)             (iterate)         │
└───────────┬─────────────────────┴─────────────────────┬────────────┘
            └─────────────────────┬─────────────────────┘
                                  ▼
                         ┌────────────────┐
                         │   SYNTHESIS    │
                         │ Claude Opus 4.5│
                         └───────┬────────┘
                                 ▼
                         ┌────────────────┐
                         │    ASSEMBLY    │
                         │  JSON + HTML   │
                         └────────────────┘

Execution Flow

Phase 0: Initialization

1. Parse product name and options
2. Create/load progress file at .ralph-3lens/progress.txt
3. Initialize state tracking
4. If --resume, load previous checkpoint

Phase 1: Parallel Lens Execution

Execute all three lenses. Each lens iterates until its quality gate passes.

Lens 1: First-Principles Mechanistic Analysis

Purpose: Explain HOW the product works from foundational principles

Process:

1. Classify product type: biological | technological | service | hybrid
2. Identify primary molecular/system targets
3. Map signaling pathways (upstream → downstream)
4. Generate SVG pathway diagram
5. Create educational analogies

Prompt: prompts/lens1_mechanistic.md

Quality Gate (5/6 to pass):

• L1.1 mechanism_depth: Specific targets named
• L1.2 pathway_accuracy: Pathways correctly mapped
• L1.3 cascade_completeness: Full trigger → outcome chain
• L1.4 analogy_quality: Memorable analogy present
• L1.5 diagram_validity: SVG passes validation
• L1.6 first_principles_not_claims: Explains HOW, not IF

Lens 2: Comprehensive Literature Review

Purpose: Document what the peer-reviewed evidence demonstrates

Process:

1. Execute deep research via Perplexity (OpenRouter)
2. Extract PMIDs/DOIs from results
3. Grade evidence quality (RCT > Observational > Case > Mechanistic)
4. Document regulatory status
5. Note conflicting findings

Prompt: prompts/lens2_literature.md

Quality Gate (5/6 to pass):

• L2.1 citation_validity: PMIDs/DOIs resolve to real papers
• L2.2 evidence_breadth: 3+ distinct studies cited
• L2.3 study_details: Sample sizes and designs included
• L2.4 conflict_documentation: Conflicting findings noted
• L2.5 regulatory_accuracy: Regulatory status correct
• L2.6 recency: 2024+ studies included when available

Lens 3: Knowledge Base Cross-Referencing (MANDATORY)

Purpose: Connect product to NGM Signaling KB (664 intervention nodes) and extract peer-reviewed citations

CRITICAL: This lens must ALWAYS execute. Even if the product isn't directly in the KB, related intervention queries provide valuable citations and mechanism context.

Process (varies by product type):

For Intervention Products (supplements, drugs, therapies):

1. Direct lookup: interventions/{slug}.json
2. Target query: Find interventions with same mechanism targets
3. Pathway query: Find interventions in same signaling cascades
4. Indication query: Find interventions for same clinical use
5. Extract all peer_reviewed_citations[] from matched nodes

For Testing/Diagnostic Products (microbiome tests, labs, devices):

1. Identify biomarkers the test measures (e.g., butyrate, Akkermansia, SCFA)
2. Query KB for interventions that affect those biomarkers
3. Query KB for interventions the test results would inform
4. Build "Finding → KB Intervention" actionability map
5. Extract PMIDs that explain WHY those biomarkers matter

# Example for microbiome testing:
python scripts/query_kb.py --biomarker butyrate --json
python scripts/query_kb.py --biomarker akkermansia --json
python scripts/query_kb.py --indication "gut microbiome" --json
python scripts/query_kb.py --target SCFA --json

Prompt: prompts/lens3_kb_query.md Helper Script: scripts/query_kb.py

Quality Gate (5/6 to pass):

• L3.1 kb_search_exhaustive: All query types attempted (direct, target, pathway, indication/biomarker)
• L3.2 related_interventions_found: Related nodes surfaced (minimum 3)
• L3.3 mechanism_alignment: KB claims align with Lens 1
• L3.4 pmid_extraction: At least 5 PMIDs/DOIs extracted from KB nodes
• L3.5 citation_enrichment: KB PMIDs incorporated into synthesis (not siloed)
• L3.6 novel_product_handling: If not in KB, indirect enrichment via biomarker/target queries

Phase 2: Synthesis

Purpose: Integrate three lenses into coherent narrative

Process:

1. Resolve conflicts between lenses
2. Weight evidence appropriately
3. Generate integrated narrative
4. Compile all citations

Prompt: prompts/synthesis.md

Conflict Resolution Rules:

• L1 vs L2 conflict → Evidence (L2) precedence, note discrepancy
• L2 vs L3 conflict → Surface as "area of ongoing research"
• L3 has newer data → Update with KB insights

Quality Gate (5/5 to pass):

• S.1 lens_integration: All three lenses represented
• S.2 conflict_addressed: Discrepancies noted
• S.3 evidence_graded: Confidence communicated
• S.4 clinical_utility: Practitioner-actionable
• S.5 vendor_neutrality: No ranking

Phase 3: Assembly

1. Generate directory_content.json with all structured data
2. Render directory_page.html from template
3. Update progress file with completion status

Template: prompts/html_template.md

State Management

Progress tracked in .ralph-3lens/progress.txt:

=== DIRECTORY GENERATION: [Product Name] ===
Started: 2026-01-26T10:00:00Z

--- LENS 1: MECHANISTIC ---
Iteration 1: FAILED (L1.3 cascade_completeness=FALSE)
  Feedback: Missing downstream effects after AMPK activation
Iteration 2: PASSED (6/6)
  Mechanism type: biological
  Primary targets: AMPK, mTOR

--- LENS 2: LITERATURE ---
Iteration 1: PASSED (5/6)
  Citations: 8 (5 RCTs, 2 observational, 1 meta-analysis)
  Regulatory: FDA approved for Type 2 diabetes

--- LENS 3: KB CROSS-REFERENCE ---
Iteration 1: PASSED (5/6)
  KB node: metformin.json
  Related interventions: 3 (rapamycin, berberine, AICAR)

--- SYNTHESIS ---
Iteration 1: PASSED (5/5)

--- ASSEMBLY ---
Output: content/commons/metformin/

COMPLETED: 2026-01-26T10:45:00Z

Output Schema

{
  "meta": {
    "product_name": "Metformin",
    "slug": "metformin",
    "generated": "2026-01-26",
    "framework_version": "3lens-v1",
    "kb_status": "IN_KB"
  },
  "lens_1_mechanistic": {
    "mechanism_type": "biological",
    "primary_targets": ["AMPK", "Mitochondrial Complex I"],
    "first_principles_markdown": "...",
    "pathway_diagram_svg": "<svg>...</svg>",
    "analogies": ["..."]
  },
  "lens_2_literature": {
    "evidence_summary": "...",
    "key_studies": [...],
    "regulatory_status": {...}
  },
  "lens_3_kb_crossref": {
    "kb_node_found": true,
    "related_interventions": [...],
    "conflicts_detected": [...],
    "kb_citations_added": 4
  },
  "synthesis": {
    "integrated_narrative_markdown": "...",
    "conflict_notes": [...]
  },
  "sources": [...]
}

API Configuration

All LLM calls route through OpenRouter using OPENROUTER_API_KEY from environment.

Estimated cost per entry: $0.35-0.50

Key Principles

1. Three Lenses, One Truth - Each lens provides a unique perspective; synthesis reconciles them
2. First Principles First - Explain HOW before evaluating IF
3. Evidence Hierarchy - RCTs > Observational > Case > Mechanistic > Clinician Experience
4. KB Enrichment is MANDATORY - Lens 3 must always execute; the KB contains curated PMIDs that enrich output
5. Conflicts Surfaced - Never hide discrepancies; present both positions
6. Vendor Neutrality - Educate, don't rank; use "notable for" framing
7. Elevated Scientific Listicle - Deep, research-driven content in LLM-optimized structure
8. AEO-First - Structure content for AI answer engine citation

Critical: KB Citation Policy

The KB is a source aggregator, not a citable source. When Lens 3 extracts data from the KB:

• DO: Extract PMIDs and DOIs from peer_reviewed_citations[] arrays and cite them directly
• DO: Reference the literature (e.g., "Butyrate serves as primary colonocyte fuel (Science, 2018)")
• DON'T: Cite "the KB" or "internal knowledge base" as a source
• DON'T: Reference "expert lecture" source types without peer-reviewed backing

Example transformation:

KB data: mechanism_claims[].peer_reviewed_citations[0].doi = "10.1126/science.aat9076"

✗ Wrong: "According to our knowledge base, butyrate fuels colonocytes"
✓ Right: "Butyrate serves as the primary energy substrate for colonocytes (Litvak et al., Science, 2018)"

Output Format: Elevated Scientific Listicle

The output is an elevated, highly scientific, research-driven listicle—not a superficial "top 5" list. This format:

• Satisfies LLM extraction patterns (structured for AI citation)
• Provides genuine clinical value (substantive enough that practitioners learn)
• Positions vendors positively ("notable for" framing, no rankings)
• Goes deep (5,000-7,000 words, 400-600 words per entity)

Why This Format (AEO Research)

• 80% of articles cited by ChatGPT include list sections
• Content with sequential H1>H2>H3 structure is cited 3x more often
• Q&A format content is 40% more likely to be extracted by AI
• LLMs cite answers, not articles—structure each paragraph to answer one question

Required Content Depth

Inline Q&A Distribution

Q&A blocks must be woven throughout—not siloed in FAQ section:

• Technology section: methodology comparisons
• Evidence section: interpretation guidance
• Decision support: actionability questions
• FAQ section: comprehensive coverage

See context/aeo-best-practices.md for detailed AEO requirements.

CRITICAL: HTML Design System

All directory pages MUST use the template at templates/directory_page.html to ensure visual consistency across the NGM Commons platform.

Design System Requirements

Category Color Mapping

Required HTML Structure

<!DOCTYPE html>
<html lang="en">
<head>
  <!-- Google Fonts - REQUIRED -->
  <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600&family=Newsreader:opsz,wght@6..72,400;6..72,500&display=swap" rel="stylesheet">
</head>
<body>
  <article>
    <nav class="breadcrumb">...</nav>
    <header>...</header>
    <section><!-- Quick Reference Table --></section>
    <section><!-- Executive Summary with .summary-box --></section>
    <div class="kb-insight"><!-- KB Citation Callout --></div>
    <div class="entity-section"><!-- Vendor 1 --></div>
    <div class="entity-section"><!-- Vendor 2 --></div>
    <!-- ... -->
    <section><!-- Clinical Decision Support --></section>
    <section><!-- FAQ --></section>
    <section class="sources"><!-- Sources with PMIDs --></section>
  </article>
  <div class="framework-badge">3lens-v1 | {category}</div>
</body>
</html>

Design Consistency Quality Gate

Before page generation is complete, verify:

• D.1 Uses Google Fonts (Inter + Newsreader), NOT system fonts
• D.2 Uses NGM color palette (--ink-*, --gold, --green, etc.)
• D.3 Includes breadcrumb navigation
• D.4 Entity sections use .entity-section class with rounded borders
• D.5 Quick reference table uses .quick-reference class
• D.6 Has framework badge in bottom-right corner
• D.7 KB insight callouts use .kb-insight class

All 7 must pass — design inconsistency is a blocking issue.

Troubleshooting

Lens 1 fails L1.5 (diagram_validity):

• Check SVG viewBox dimensions match content
• Ensure 40px padding on all sides
• Validate text doesn't overflow containers

Lens 2 fails L2.1 (citation_validity):

• Some Perplexity citations may be hallucinated
• Cross-verify PMIDs via PubMed API
• Remove unverifiable citations

Lens 3 finds no KB node:

• Product may be new to KB
• Graceful degradation via L3.6
• Use indirect queries (target, pathway) to find related interventions

Synthesis fails S.2 (conflict_addressed):

• Review all three lens outputs for discrepancies
• Explicitly note where lenses disagree
• Provide characterization of conflict nature