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Variation Spdi To Rsids

variation_spdi_to_rsids
Read-onlyIdempotent

Look up the dbSNP rsIDs that a SPDI allele maps to, via NCBI Variation Services. AUTHORITATIVE for the reverse direction — you have a genomic coordinate and alleles from a VCF or a pipeline and need the rsID other databases key on. SPDI is 0-BASED, unlike HGVS: "NC_000007.14:140753335:A:T" is the same variant as "NC_000007.14:g.140753336A>T".

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
spdiYesSPDI as seq_id:position:deleted:inserted, 0-based position. e.g. "NC_000007.14:140753335:A:T".

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false, so safety is covered. The description adds valuable behavioral context: it calls NCBI Variation Services, is authoritative in the reverse direction, and warns about the 0-based vs HGVS coordinate discrepancy with a concrete example. No contradiction with annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three tight sentences with no filler. The core action and source are front-loaded, the use case follows, and the critical coordinate-system caveat gets a concrete example. Every sentence earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a single-parameter read-only lookup tool with a fully documented schema, this is nearly complete. It covers what the tool does, when to use it, and the key input nuance. The main omission is return behavior (e.g., whether multiple rsIDs or no match are possible), but this is minor given the tool's simplicity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3. The description adds meaning beyond the schema by explaining the practical difference from HGVS and showing the exact equivalent variant in both coordinate systems, which helps avoid off-by-one errors.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb and resource: 'Look up the dbSNP rsIDs that a SPDI allele maps to.' It clearly differentiates itself from sibling tools by emphasizing SPDI's 0-based convention and the 'reverse direction' role, so an agent can tell it apart from variation_hgvs_to_spdi and variation_refsnp.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It gives an explicit use case: 'you have a genomic coordinate and alleles from a VCF or a pipeline and need the rsID other databases key on.' It does not name the sibling tools directly or state when not to use them, but the reverse-direction framing and HGVS contrast provide strong contextual guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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