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BioMCP

by yeyuan98
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TypeScript
Remote

gtex_eqtl

Read-only

Retrieve significant cis-eQTL associations for a gene in a chosen GTEx tissue, returning variant IDs, p-values, and effect sizes sorted by ascending p-value to identify regulatory variants.

Instructions

Get significant cis-eQTL associations for a gene in a specific GTEx tissue (GTEx Analysis v10): variant_id, p_value, and NES (effect direction/size), sorted by ascending p-value.

tissue is a required GTEx tissueSiteDetailId (e.g. Whole_Blood, Brain_Cortex).

An empty associations list is a VALID scientific result — the gene was tested but has no significant cis-eQTLs in that tissue (not a lookup failure). In that case the result carries a note listing other tissues where significant eQTLs DO exist (or stating that none exist in any tissue).

Input Schema

NameRequiredDescriptionDefault
geneYesHGNC symbol (TP53) or Ensembl gene ID (ENSG00000141510, versioned or bare)
limitNoMaximum associations to return
tissueYesGTEx tissueSiteDetailId — required, e.g. Whole_Blood

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed2 schema fields changedv1.6.0-alpha.7
    • addedInput schema / properties / gene / minLength
      Added value: +1
    • addedInput schema / properties / tissue / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint and openWorldHint, so safety is covered; the description adds genuinely new behavioral context beyond that — results are pre-filtered to significant associations, sorted ascending by p-value, and empty results carry an explanatory note rather than signaling failure. It does not mention the limit's truncation effects or pagination, but the value added is substantial.

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 short, front-loaded blocks: what it returns and how it's sorted first, required-parameter format second, and the empty-result caveat last. Every sentence carries operational value, with no filler.

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

Completeness5/5

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

With no output schema, the description carries the return-value burden and does so completely: named fields, sort order, and the meaning of an empty result plus its accompanying note. An agent has everything needed to call it and interpret the response.

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%, so gene, tissue, and limit are already documented; the description only reinforces tissue examples and format. It adds marginal param meaning (significance filtering and ascending p-value ordering) rather than new per-parameter semantics, so the baseline 3 applies.

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?

States a specific verb+resource ('Get significant cis-eQTL associations for a gene in a specific GTEx tissue') and enumerates the returned fields with a defined sort order. It is clearly distinguishable from sibling gtex_expression (expression levels) and from variant-level tools.

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?

Gives concrete usage context: tissue is required and must be a GTEx tissueSiteDetailId, with examples. It anticipates the main misread (empty list = valid negative result) and explains the fallback note. It does not explicitly route to an alternative tool (e.g., gtex_expression) when the goal is expression rather than eQTLs.

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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