| name | genome-create |
| description | Create gene, system, or phenotype notes from SQLite genotype data and templates.
Triggers on: /new-gene SYMBOL, /new-system NAME, "add gene X", "create system note",
"create phenotype note for X".
|
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:
- What This Gene Does — biology, function, mechanism
- Personal Genotype — table from SQLite data with evidence tiers
- Health Relevance — by domain subsections
- Drug Interactions — table if applicable
- Gene-Gene Interactions — cross-references to existing vault genes
- What Changes This — modifiable factors (BDNF exit ramp philosophy)
- Confidence & Caveats — evidence tier, limitations, link to [[Genetic Determinism - Limits and Caveats]]
- 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)
