Nutrigenomics

Nutrigenomics

Use this skill when the user asks how a germline variant affects nutrient metabolism, food tolerance, or taste perception within declared domains:

• folate metabolism
• vitamin D status
• iron storage
• lactose tolerance
• lipid diet response (APOE e2/e3/e4)
• obesity predisposition (single-marker context only)

Out of scope — refuse, do not approximate

Do NOT use this skill for, and DO surface as refusals:

• Macronutrient ratio prescriptions ("eat X% fat because of your APOE")
• Specific supplement dosing recommendations
• Weight-loss outcome prediction from genotype
• Diet-matching to genotype for fitness goals
• Microbiome-mediated dietary effects
• "Methylation cycle" prescriptions beyond folate marker context
• General health-outcome prediction from a small marker set
• "Detox capacity" framings
• Food allergy risk prediction
• Vitamin megadose prescriptions

The capability returns coverage_status: out_of_scope_for_input for these domain ids. Treat the refusal literally — do not reach for adjacent records that look similar.

Contract

• Reads public catalogue metadata only; does not read an Active Genome Index.
• For scanning an active genome, compose with active_genome_index.classify_genotype_support using the variant coordinates carried in each record.
• For stratified allele frequencies, call gnomad.fetch_population_frequency.
• For primary GWAS effect sizes, call gwas.compare_variant_associations using the gwas_catalog_id carried in each record's downstream_traits_with_gwas.

Convention: See skills/conventions/context-routing.md. Convention: See skills/conventions/evidence-quality.md. Convention: See skills/_output-rules.md.

First Actions

1. If the request is shaped like a diet prescription, supplement dosing, weight-loss prediction, or any item in the out-of-scope list, refuse first. Do not call retrieval tools.
2. Use nutrigenomics.list_domains to confirm the relevant domain is declared and to inspect evidence-tier counts before drilling in.
3. Use nutrigenomics.build_source_context when grounding a discussion in provenance is needed — e.g. when a user asks where the records come from or why diet prescriptions are out of scope.
4. Use nutrigenomics.retrieve_domain_markers with the validated domain_id. Default min_evidence_tier="established". Loosen to "probable" only when the question explicitly invites less-replicated evidence.
5. Use nutrigenomics.retrieve_variant_records when the agent already has an rsID and wants to know which declared domains reference it.

Interpretation Rules

• Each record carries out_of_scope_claims. Surface these as explicit disclaimers — do not paraphrase around them.
• evidence_tier is literal. An emerging record is not equivalent to an established one; hedge in any agent-generated text accordingly.
• Single-marker evidence does not substitute for measured lab values (serum 25(OH)D, ferritin/transferrin saturation, homocysteine, lipid panel) when clinical decisions are at stake.
• Absence of a marker from the catalogue is not evidence of negligible effect — the catalogue is intentionally small and curated.

User-Facing Answer Shape

Do not add a routine Active Genome Index status line for these public catalogue tools. For each cited marker:

• Variant identifier (rsID + gene)
• Established effect (single sentence)
• Evidence tier
• One or two of the most relevant out_of_scope_claims as disclaimers
• The single most relevant lab measurement that should accompany the marker (when applicable: homocysteine for MTHFR, 25(OH)D for vitamin D markers, ferritin + transferrin saturation for HFE)

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

nutrigenomics.build_source_context

Explain nutrigenomic catalogue provenance, domain definitions, evidence-tier meanings, method limitations, and the non-prescription boundary.

Use when: The user or agent asks what the nutrigenomics catalogue is, where the records come from, what evidence tiers mean, or why the capability refuses diet prescriptions.

Why necessary: Nutrigenomic language is easy to overstate. Explicit source context grounds the agent in the boundary before it interprets records.

Not for: Returning marker records; use nutrigenomics.retrieve_domain_markers or nutrigenomics.retrieve_variant_records.

Example prompts: Explain the source and limitations of Genomi's nutrigenomic catalogue.

Result semantics: Public metadata only. Returns capability provenance, declared domains, evidence-tier definitions, out-of-scope-by-construction items, and the non-prescription boundary note.