Allen Brain API MCP Server

get_structure_graphs

Retrieves brain structure graphs from the Allen Brain ontology to explore hierarchical relationships between anatomical regions. Control output size with the number of rows parameter.

Instructions

Retrieve structure graphs (from OntologiesApi).

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "get_structure_graphs"
  }
}

Input Schema

Name	Required	Description	Default
`numRows`	No	Maximum number of rows (default is 50).

Schema Changelog

Changes observed during successful MCP inspections.

First observedv1.0.0May 29, 2026

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. It only states 'Retrieve', implying a read operation, but does not disclose any behavioral traits such as side effects, rate limits, or authentication requirements. Minimal transparency.

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?

Single sentence, no wasted words. Efficiently conveys the core action, though it is sparse on details.

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 no output schema and simple input, the description lacks explanation of return format, what a structure graph is, or any usage context. It is insufficient for full understanding.

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 coverage is 100% with one parameter 'numRows' already described. The description adds no extra context beyond the schema, so baseline score of 3 is appropriate.

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?

Description clearly states the action ('Retrieve') and resource ('structure graphs') with source ('OntologiesApi'), providing a clear purpose. However, it does not differentiate from sibling tools like 'get_structures' or specify what a structure graph represents, lacking nuance.

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 on when to use this tool versus alternatives. Does not mention context, prerequisites, or exclusions. The agent receives no help to decide between this and similar retrieval tools.

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