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BioMCP

by yeyuan98
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TypeScript
Remote

gtex_expression

Read-only

Retrieve median GTEx gene expression across 54 tissues by HGNC symbol or Ensembl ID, sorted highest first, and filter results to a specific tissue site.

Instructions

Get median gene expression across GTEx tissues (GTEx Analysis v10, 54 tissue sites, TPM, sorted highest first).

Accepts an HGNC symbol (TP53) or Ensembl gene ID (ENSG00000141510, versioned or bare). Optionally filter to a single tissue via its tissueSiteDetailId (e.g. Brain_Cortex, Whole_Blood).

Input Schema

NameRequiredDescriptionDefault
geneYesHGNC symbol (TP53) or Ensembl gene ID (ENSG00000141510, versioned or bare)
limitNoMaximum tissues to return (highest expression first)
tissueNoGTEx tissueSiteDetailId filter, e.g. Brain_Cortex, 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. Changed1 schema field changedv1.6.0-alpha.7
    • addedInput schema / properties / gene / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered; the description adds real context on top: dataset version (v10), 54 tissue sites, TPM normalization, and descending sort order. It stops short of noting that the default limit (20) truncates below the full 54 tissues or what occurs for an unknown gene/tissue.

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?

Two tight sentences, zero filler, with the core operation and dataset scope front-loaded and the input/optional-filter details second. Every clause (v10, 54 tissues, TPM, sort order) carries information an agent can act on.

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?

With no output schema, the description usefully characterizes the return (median TPM per tissue, ordered highest first). It is nearly complete for a read-only lookup, but omits how limit interacts with the 54-tissue ceiling and what the response looks like when a gene or tissue matches nothing.

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 all three parameters are already documented in the schema, and the description largely restates them (gene formats, tissue example). It adds no semantics beyond the schema, such as case sensitivity for tissue IDs or how invalid tissue strings are handled, so baseline 3 applies.

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

Purpose4/5

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

States a specific verb and resource ('Get median gene expression across GTEx tissues') plus concrete dataset facts: GTEx Analysis v10, 54 tissue sites, TPM units, sorted highest first. That is enough to separate it from the only close sibling, gtex_eqtl, but the description never names that sibling or explicitly contrasts expression levels with eQTL associations.

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

Usage Guidelines3/5

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

Usage is only implied: accepts an HGNC symbol or Ensembl ID and optionally a tissueSiteDetailId filter. There is no statement about when to prefer this over gtex_eqtl, gene_get, or ensembl_lookup, and no guidance on behavior when a gene has no GTEx data.

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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