Genome Onboard

Genome Onboard

Set up a personalized genome vault based on health goals, self-assessment, and imported genotype data.

Prerequisites

• Genome data already imported via genome-import (SQLite database populated)
• Obsidian vault initialized from vault-template/

Preflight Validation

Before onboarding begins, run the automated prerequisite checker. This replaces manual verification and catches common setup issues early.

python3 scripts/check_prerequisites.py --vault ~/Brains/genome --db data/genome.db

The checker validates:

• Vault structure — expected directories exist (Genes/, Guides/, Reports/, Templates/)
• Community plugins enabled — .obsidian/community-plugins.json exists and is non-empty
• Dataview installed (critical) — MoC pages and dashboards depend on it
• Templater installed (optional) — warns if missing
• Database populated — genome.db exists and has variant data

When run via scripts/onboard.py, these checks execute automatically at the start. If any critical check fails, onboarding aborts with fix instructions. Use --skip-checks to bypass (not recommended).

If the database check fails, tell the user:

It looks like you haven't imported your genome data yet. Run /genome-import first — onboarding needs your genotype data to create personalized content.

If the Dataview check fails:

Community plugins or Dataview are not set up. Without Dataview, the Dashboard and MoCs will appear empty after onboarding. See [[Getting Started]] Step 1.

Vault Configuration

• Config: $GENOME_VAULT_ROOT or config/default.yaml
• Database: data/genome.db
• Goal map: config/goal_map.yaml
• Interview questions: skills/genome-onboard/references/interview_questions.yaml
• Templates: Templates/

Modes

Quick Mode (default, ~2 min)

/genome-onboard or /genome-onboard --quick

4 questions → vault bootstrap (8-12 gene notes, Wallet Card). Use when the user wants to get started fast.

Full Mode (~12 min)

/genome-onboard --full

22 questions across 4 phases → Profile Card + personalized Action Plan + vault bootstrap. Includes validated instruments (GAD-7, PHQ-2, PSS-4). Use when the user wants a comprehensive profile.

Quick Mode Workflow

Step 1: Health Goal Questionnaire

Ask the user 4 questions using AskUserQuestion:

1. What matters most? (multi-select from goal_map.yaml):

   • Medication safety
   • Mental health (anxiety/mood)
   • Addiction recovery
   • Liver health
   • Gut health / autoimmune
   • Sleep optimization
   • Cardiovascular / metabolic
   • Comprehensive (everything)

2. Current medications/substances (free text):

   • Prescription drugs (SSRIs, statins, etc.)
   • OTC drugs (NSAIDs, PPIs)
   • Supplements
   • Cannabis, alcohol, caffeine

3. Active diagnoses or symptoms (free text):

   • GAD, IBS, insomnia, joint pain, etc.

4. Do you have recent lab results? (yes/no):

   • If yes, suggest running /biomarker after onboarding

Step 2: Map Goals to Targets

Load config/goal_map.yaml and resolve:

• target_systems — biological systems to document
• seed_genes — genes to create notes for
• first_reports — reports to generate
• first_tests — decision-changing tests to recommend
• first_protocols — protocols to create

Step 3: Score and Prioritize Genes

Query SQLite for available genotype data on seed genes:

sqlite3 data/genome.db "SELECT rsid, genotype, source, r2_quality FROM snps WHERE rsid IN (SELECT rsid FROM genes WHERE gene_symbol='CYP2D6')"

Score each gene using weights from config/goal_map.yaml:

score = 8*medication_match + 6*goal_match + 5*severe_finding + 4*protocol_exists + 3*biomarker_link + 2*evidence_weight

Cap at 8-12 genes for initial generation. Always include safety-critical PGx genes if medication_safety is selected.

Step 4: Generate First Outputs

Always generate:

1. Wallet Card (Reports/Wallet Card.md) — emergency drug safety reference
2. Top Tests section in Action Items — decision-changing labs based on goals

Goal-dependent: 3. 8-12 Gene notes — use /new-gene workflow for each, prioritized by score 4. 2-4 System notes — use Templates/_System.md 5. 2-3 Protocol notes — use Templates/ or create from goal_map

Step 5: Populate Dashboard

Update Dashboard.md with:

• User's selected goals
• Profile name and import stats
• Goal-specific quick access links
• Progress tracking (X/Y genes created)

Step 6: Wire Navigation

• Update MoC - All Genes.md (Dataview auto-populates)
• Update MoC - All Systems.md (Dataview auto-populates)
• Create relevant entries in Action Items.md
• Link first reports from Dashboard

Step 7: Suggest Next Steps

Based on genotype findings, suggest:

• Specific lab tests (with reasoning)
• Follow-up gene notes to create
• Whether imputation would unlock more data
• Prescriber conversation topics

Quick Mode Output

• Populated vault with 8-12 gene notes, 2-4 system notes, Wallet Card
• Dashboard.md personalized to user goals
• Action Items with prioritized tests and prescriber topics
• Getting Started guide with user's specific next steps

Full Mode Workflow

Load interview questions from references/interview_questions.yaml.

Phase 1: Quick Profile (2 min, 4 questions)

Same as Quick Mode Steps 1-4 above. Collect goals, medications, diagnoses, lab status.

Phase 2: Physiological Assessment (5 min, 10 questions)

Ask using AskUserQuestion, one at a time or grouped:

5. Sleep duration (hours)
6. Sleep quality (1-5)
7. Wake time consistency
8. Exercise: type, frequency, time of day
9. Caffeine: cups/day, last intake
10. Alcohol: drinks/week
11. Cannabis: current use, frequency
12. GI symptoms: Bristol scale, frequency
13. Pain: locations, NSAID response
14. Morning stiffness: duration

Each question has gene_context in the YAML — use this to explain WHY the question matters:

"I'm asking about caffeine because your CYP1A2 genotype affects how fast you metabolize it — this shapes your caffeine protocol."

Phase 3: Psychological Assessment (3 min, 4 instruments)

15. GAD-7 — Present all 7 items, score 0-3 each. Total → severity band.
16. PHQ-2 — 2 items, flag if score >= 3 (recommend full PHQ-9).
17. PSS-4 — 4 items perceived stress.
18. Medication satisfaction (1-5 Likert).

Important: Frame these as "baseline for tracking change over time", not diagnosis. Include standard clinical disclaimers.

Phase 4: Context & History (2 min, 4 questions)

19. Family history (multi-select)
20. Ancestry (free text, for PRS calibration)
21. Prior genetic testing
22. Main concerns / questions

Step A: Generate Profile Card

Create Reports/Profile Card.md from Templates/_Profile Card.md:

• Populate all frontmatter fields from interview responses
• Calculate assessment scores (GAD-7 total, PHQ-2 flag, PSS-4 total)
• Map sleep/exercise/substance data to gene context
• Flag any red-zone values (sleep <6h, GAD-7 >= 15, Bristol >= 6)

Step B: Apply Assessment Modifiers

Load assessment_modifiers from interview_questions.yaml. For each modifier:

• Evaluate condition against collected data
• If true: boost specified genes in scoring, add recommended protocols/tests

Example: if gad7_score >= 10, boost FKBP5/SLC6A4/CRHR1 by +3 and add GAD Protocol.

Step C: Generate Action Plan

Create Reports/Action Plan.md:

1. Your Genetic Profile Summary — 3-5 sentences, plain language, no rsIDs

   • Top 3 strengths (from genotype + assessment context)
   • Top 3 watchpoints (genotype × assessment interaction)

2. Priority Actions — Scored by: evidence_tier × assessment_severity × gene_actionability

   • Each: what to do, why (gene basis), when, evidence tier
   • Personalized by assessment (high GAD-7 → different priorities than low)

3. Tests to Request — Filtered from Complete Testing Guide by profile

   • Only tests relevant to this person's goals + findings

4. Medication Review — Drug-gene interactions for listed medications

   • Metabolizer status for each relevant CYP
   • Optimization suggestions for prescriber conversation

5. 30-Day Protocol — Concrete daily actions

   • Morning routine (chronotype + exercise timing)
   • Supplement stack (genotype + current status)
   • Monitoring targets tied to genetics

6. What to Track — Metrics for reassessment

   • HRV (if Apple Watch) → FKBP5, CRHR1
   • Sleep duration → CYP1A2, melatonin dosing
   • GI symptoms → ATG16L1, FUT2
   • GAD-7 retest at 30 days

Step D: Run Quick Mode Steps 2-7

Generate gene notes, system notes, Wallet Card, wire navigation — same as Quick Mode but with assessment-boosted gene priorities.

Step E: Video Export (optional)

If user wants a video summary:

python3 scripts/export_video_data.py --profile-card "Reports/Profile Card.md" --action-plan "Reports/Action Plan.md" --output data/video_data.json

Then render with Remotion (requires Node.js + Remotion setup):

cd video && npx remotion render GenomeReport --props data/video_data.json

Or use /videopublish skill for full YouTube pipeline.

Full Mode Output

• Everything from Quick Mode, PLUS:
• Reports/Profile Card.md — structured self-assessment with gene context
• Reports/Action Plan.md — personalized, assessment-weighted action plan
• Assessment scores stored in Profile Card frontmatter for longitudinal tracking
• Optional: MP4 video summary via Remotion

Next Steps (show after onboarding completes)

After onboarding finishes, display the following to the user:

Your vault is ready. Here's what to do next:

1. **Read your Wallet Card** — open Reports/Wallet Card.md.
   This is your emergency drug safety reference. Consider printing it
   or saving a photo on your phone.

2. **Review your Dashboard** — open Dashboard.md.
   This is your home base. It shows your goals, top genes, and action items.

3. **Check Action Items** — open Action Items.md.
   These are lab tests and prescriber conversations prioritized by your
   genetics. The top 2-3 items are the most decision-changing.

4. **Explore a gene note** — pick the highest-scored gene from your
   Dashboard and read through it. Each note explains what your genotype
   means, what the evidence says, and what you can do about it.

5. **Import lab results** (if you have them) — run /biomarker.
   Combining genetics with actual bloodwork is where the real insights are.

For the full setup checklist, see Guides/Setup Checklist.md.
For detailed guidance on any step, see Guides/Getting Started.md.