Genomi Decode

Genomi Decode

The /genomi decode kicker tells the agent to assemble every relevant Genomi capability's evidence about the user's active genome and emit a single self-contained Genomi Dashboard.html artifact. Activate this skill whenever the user types /genomi decode, asks for "the dashboard", asks to "decode my genome", or asks for a one-shot evidence rundown.

Activation

This skill requires an Active Genome Index session and explicit approval to read it. The same approval gate that protects variant.resolve, clinvar.*, and the PGx ops protects decode.render_dashboard. If no active genome is selected the op fails with active_genome_index_required; if approval has not been granted it fails with active_genome_index_approval_required.

Reconcile Active Genome Index lifecycle before gathering panels

Call genomi.describe_context first. If active_genome_index.active_genome_index_readiness.status is needs_reparse or schema_too_new, handle the lifecycle before gathering any panel evidence — do not proceed with a stale Active Genome Index and silently bound the panels.

The full procedure lives in the Active Genome Index skill under the lifecycle guidance for needs_reparse and schema_too_new. Summary for decode:

1. If needs_reparse and availability.agi_intake_source_path is true, call genomi.parse_source({"source": active_genome_index.agi_intake_source_path}) without prompting. Routine maintenance.
2. If needs_reparse and the source path is gone, ask the user once for the current path and parse that. Don't continue with a stale Active Genome Index.
3. If schema_too_new, the user's runtime is out of date — tell them to upgrade Genomi, stop.
4. Only after active_genome_index_readiness.status == "complete" call the decode operation.

Dashboard Build

Call decode.render_dashboard. Decode owns panel gathering, panel shaping, and rendering. The agent may choose dashboard categories through structured parameters such as panels and select declared score/domain options. Omitted panels means every dashboard category. The agent does not assemble panel evidence and does not ask which PGx route to run; decode owns that work.

The renderer normalizes native upstream-op shapes internally:

• overview — adapts active_genome_index.summarize output; snake_case keys (genome_build, nickname, active_genome_index_completed_at, nearest_reference_groups) are mapped automatically.
• variants — adapts clinvar.scan_candidates variant inventory rows; clinvar.match_variants JSONL rows ({sample_variant, clinvar}) are also handled. Carrier/condition review groups render under risk, not variants.
• nutrigenomics — adapts nutrigenomics.retrieve_domain_markers; it extracts gene.symbol, variant.rsid, established_effect.claim (→ recommendation), evidence_tier, and domain label (→ marker).
• ancestry — adapts ancestry.estimate_population_context.
• pgx — adapts PharmCAT sample_pgx_matrix and medication-review medication_review_matrix rows into PGx cards without merging separate medication recommendations by gene alone.
• risk — adapts native prs.calculate_score results and phenotype.plan_risk_investigation carrier/condition review rows into risk/review cards.
• variants_all — uses the ClinVar matches JSONL path materialized by decode.

Decode also gathers the current carrier/condition and PGx review contracts:

• For risk, decode runs the declared risk_review_types from the selected Active Genome Index ClinVar matches scope. Omitted risk_review_types means carrier_review plus observed_condition_review; pass an empty array only when the user wants PRS-only risk evidence.
• For pgx, decode runs pharmacogenomics.review_medication for explicit pgx_review_targets and for drug/gene targets discovered in PharmCAT sample_pgx_matrix rows, up to pgx_review_target_limit. Gene-only sample rows can be preserved as sample evidence, but decode does not invent medication-specific recommendations without a declared drug/source target.

If no PRS scores are installed in the user's library, the builder supplies a typed empty risk state so stale risk evidence is cleared rather than preserved.