Genome Create

Genome Create

Create structured vault notes from genotype data, following templates and evidence standards.

Vault Configuration

• Database: data/genome.db (query genotype data FIRST, never guess)
• Templates: Templates/_Gene.md, Templates/_System.md, Templates/_Phenotype.md
• Evidence tiers: config/evidence_tiers.yaml

Workflow: Gene Note

Step 1: Identify Gene

User specifies gene symbol (e.g., CYP2D6, BDNF, APOE).

Step 2: Query SQLite

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

If gene not in genes table, search by chromosome region:

sqlite3 data/genome.db "SELECT rsid, genotype, r2_quality FROM snps WHERE chromosome='CHR' AND position BETWEEN START AND END AND r2_quality > 0.8"

Step 3: Research Context

• Check existing vault notes for cross-references
• Look up gene in enrichments table
• Note drug interactions (CPIC/DPWG if pharmacogene)

Step 4: Create Note

Follow template exactly (Templates/_Gene.md). Required sections:

1. What This Gene Does — biology, function, mechanism
2. Personal Genotype — table from SQLite data with evidence tiers
3. Health Relevance — by domain subsections
4. Drug Interactions — table if applicable
5. Gene-Gene Interactions — cross-references to existing vault genes
6. What Changes This — modifiable factors (BDNF exit ramp philosophy)
7. Confidence & Caveats — evidence tier, limitations, link to [[Genetic Determinism - Limits and Caveats]]
8. Sources — real published citations only

Step 5: Wire Navigation

• Add to relevant System notes' genes: frontmatter
• Update MoC (Dataview handles automatically)
• Cross-link to related Phenotype notes

Step 6: Validate (optional)

If genome-validate is configured, run validation on the new note.

Rules

• Query SQLite FIRST — never guess genotypes
• Every claim needs an evidence tier (E1-E5)
• Gene-gene interactions must reference existing vault genes
• Always end with what can change (the exit ramp)
• For imputed variants: always note r2_quality, flag if < 0.8
• Use experience-based naming for phenotypes, not deficit language

Workflow: System Note

Similar but uses Templates/_System.md. Aggregates genes by biological system.

Workflow: Phenotype Note

Uses Templates/_Phenotype.md. Bridges genetics to lived experience.

Output

• New note at Genes/SYMBOL.md, Systems/Name.md, or Phenotypes/Name.md
• Updated cross-references in related notes
• Validation report (if enabled)