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Variation Hgvs To Spdi

variation_hgvs_to_spdi
Read-onlyIdempotent

Normalize an HGVS expression to SPDI (sequence-position-deletion-insertion) contextual alleles via NCBI Variation Services. AUTHORITATIVE for turning a clinician- or paper-style variant string ("NC_000007.14:g.140753336A>T", "NM_004333.6:c.1799T>A") into the canonical, left-shifted coordinate form that dbSNP/ClinVar keys on, and for validating that an HGVS string is well-formed at all.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
hgvsYesHGVS expression on a RefSeq accession, e.g. "NC_000007.14:g.140753336A>T" or "NM_004333.6:c.1799T>A".

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already cover read-only, idempotent, and non-destructive behavior. The description adds valuable behavioral context beyond annotations: it calls out the NCBI Variation Services dependency, the canonical left-shifted output, and the validation capability. No contradictory signals exist.

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

Conciseness4/5

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

The description is compact and front-loads the core action. The examples and explanatory clauses are useful rather than filler, though the second sentence is somewhat dense and could be tightened without losing meaning.

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 normalization tool with no output schema, the description covers input conventions, the transformation performed, the output's coordinate style, and the validation use case. It does not enumerate error behavior or exact response shape, but the simplicity of the tool makes this gap minor.

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

Parameters3/5

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

Schema description coverage is 100%, and the single 'hgvs' parameter is already documented with examples in the schema. The description reinforces the input style ('clinician- or paper-style variant string') but does not add substantially new parameter-level meaning beyond what the schema provides. Baseline 3 is appropriate.

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 starts with a specific verb and resource: 'Normalize an HGVS expression to SPDI...' It then clarifies the exact type of input strings and the canonical coordinate form produced. This clearly differentiates it from sibling tools like variation_refsnp and variation_spdi_to_rsids, which handle different variant representations.

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?

The description gives clear context for when to use the tool: when converting clinician- or paper-style HGVS strings into dbSNP/ClinVar keyed coordinates, and for validating HGVS well-formedness. It does not explicitly name alternative tools or exclusion conditions, but the stated scope is strong enough that an agent can infer appropriate use.

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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