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AGR MCP Server

AGR MCP Server

by nuin
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Remote

search_alleles

Find alleles and genetic variants in the Alliance of Genome Resources database to support genomics research across multiple model organisms.

Instructions

Search for alleles/variants in the Alliance database.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>"
    },
    "name": "search_alleles"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesAllele name or keyword
limitNoMaximum results

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv5.0.2

TDQS

C2.9/5.0
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It only states the search function without details on permissions, rate limits, result format, or pagination. For a search tool with zero annotation coverage, this is inadequate.

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?

The description is a single, efficient sentence that directly states the tool's purpose without unnecessary words. It is appropriately sized and front-loaded, making it easy to parse quickly.

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

Completeness2/5

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

Given the complexity of a search tool with no annotations and no output schema, the description is incomplete. It lacks information on behavioral traits, result structure, and usage context, which are essential for effective tool invocation.

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%, with clear descriptions for 'query' and 'limit' parameters. The description adds no additional meaning beyond the schema, such as query syntax examples or result ordering. Baseline 3 is appropriate when the schema does the heavy lifting.

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?

The description clearly states the action ('Search for') and resource ('alleles/variants in the Alliance database'), making the purpose understandable. However, it doesn't distinguish this tool from sibling tools like 'search_genes' or 'search_diseases', which also search the same database but for different resources, so it lacks sibling differentiation.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It doesn't mention sibling tools like 'get_gene_alleles' for allele retrieval by gene or 'mine_search' for broader queries, leaving the agent without context for tool selection.

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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