MyGene MCP Server

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query_genes

Search genes by identifiers or keywords and retrieve annotations, expression, pathways, variants, and more from multiple biological databases.

Instructions

Search for genes using the MyGene.info query API.

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": {
      "q": "<q>"
    },
    "name": "query_genes"
  }
}

Input Schema

Name	Required	Default
`q`	Yes
`size`	No
`sort`	No
`from_`	No
`facets`	No
`fields`	No	symbol,name,taxid,entrezgene
`species`	No
`fetch_all`	No
`scroll_id`	No
`facet_size`	No

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.3.0Aug 6, 2026

TDQS

C2.4/5.0

Behavior2/5

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

With no annotations, the description must disclose behavioral details, but it only says 'Search for genes' — implying a read operation without stating pagination, rate limits, return format, or any special behavior of the MyGene.info API. The mention of the API name provides minor context but no actionable transparency about side effects or limitations.

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

Conciseness3/5

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

The description is a single, grammatically simple sentence with no wasted words, making it easy to parse. However, it is under-specified for a tool with 10 parameters and numerous siblings; conciseness here is due to brevity rather than well-structured, high-information density.

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

Completeness1/5

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

The tool is complex: 10 parameters, no annotations, and an output schema that is present but not described. The description provides almost no operational context—no query construction examples, no parameter semantics, no mention of default behavior or how to filter by species. It is inadequate for an agent to use effectively.

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

Parameters1/5

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

Schema description coverage is 0%, so the description should explain parameter meanings, but it mentions none of the 10 parameters. 'q', 'species', 'fields', and 'fetch_all' all remain undefined in the description, leaving the agent to infer semantics solely from the bare schema. This is a complete failure to compensate for missing schema descriptions.

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 states a clear action: 'Search for genes' using the MyGene.info query API. It identifies the resource (genes) and the operation (search), making the primary purpose evident. However, it does not differentiate from the many sibling query tools, such as query_genes_batch or query_with_filters.

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?

No guidance is provided on when to use this tool versus alternatives. Given the large set of sibling tools (query_genes_batch, query_genes_by_disease, search_by_field, etc.), the description should explain that this is the general-purpose gene search endpoint or indicate specific scenarios. It simply states what it does, leaving usage decisions entirely to the agent.

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