exon-research/genomi/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.

1. Use nutrigenomics.list_domains to confirm the relevant domain is

declared and to inspect evidence-tier counts before drilling in.

1. 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.

1. 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.

1. 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.

nutrigenomics.list_domains

List declared nutrigenomic domains with evidence-tier coverage and explicit out-of-scope-by-construction notes.

Use when: The user asks what nutrigenomic domains Genomi covers, or the host agent needs to validate that a domain is in scope before retrieving markers.

Why necessary: Nutrigenomics is a pseudoscience-prone domain. Listing declared domains and explicit out-of-scope-by-construction items lets the agent refuse out-of-scope questions before reaching for marker records.

Not for: Returning specific marker records; use nutrigenomics.retrieve_domain_markers. Diet prescriptions, supplement dosing, weight-loss prediction.

Example prompts: What nutrigenomic domains does Genomi cover? Is weight-loss diet matching in scope for Genomi nutrigenomics?

Result semantics: Returns the declared domain catalogue, evidence-tier counts per domain, the out-of-scope-by-construction list, and the non-prescription boundary note.

nutrigenomics.retrieve_domain_markers

Retrieve curated single-marker records for a declared nutrigenomic domain, filtered by minimum evidence tier.

Use when: The host agent needs curated single-marker evidence for a declared domain (folate_metabolism, lactose_tolerance, iron_storage, vitamin_d_status, lipid_diet_response, obesity_predisposition).

Why necessary: Returns evidence-tiered records with explicit out_of_scope_claims so the agent can ground a nutrient/tolerance discussion without propagating pseudoscience claims about the variant.

Not for: Diet prescriptions, supplement dosing, weight-loss prediction. Polygenic risk scoring; this is single-marker evidence only. Genome scanning; compose with active_genome_index.classify_genotype_support using the variant coordinates from each record. Population-stratified allele frequencies; use gnomad.fetch_population_frequency. Primary GWAS effect sizes; use gwas.compare_variant_associations with the gwas_catalog_id from downstream_traits_with_gwas.

Example prompts: What does Genomi have on folate_metabolism markers? Retrieve established-tier iron_storage records.

Result semantics: Each record carries variant identifiers, established_effect with GWAS Catalog chain-out, evidence_tier, resolvable source citations, established_caveats, and out_of_scope_claims. The agent must surface out_of_scope_claims as disclaimers rather than paraphrase around them.

nutrigenomics.retrieve_variant_records

Retrieve any nutrigenomic catalogue records referencing a specific rsID.

Use when: The host agent has a specific variant identifier and wants to know whether the nutrigenomic catalogue carries any records for it.

Why necessary: A variant may participate in more than one declared domain. Variant-anchored lookup surfaces all matching curated records at once.

Not for: Variant resolution from coordinate to rsID; use variant.resolve first. Variants outside declared nutrigenomic domains; in_scope_empty indicates the catalogue does not cover the variant.

Example prompts: What does Genomi say about rs1801133 nutrigenomically? Are there nutrigenomic records for rs429358?

Result semantics: Returns one or more curated records referencing the variant. coverage_status='in_scope_empty' when the variant is not in the catalogue; absence is not evidence of negligible effect.