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Allen Brain API MCP Server

by maflot

get_structures

Retrieve anatomical structure data from the Allen Institute ontology. Optionally filter by structure graph ID and limit the number of rows.

Instructions

Retrieve data about anatomical structures (from OntologiesApi).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
graphIdNoFilter by a specific structure graph id.
numRowsNoMaximum number of rows (default is 50).
Behavior2/5

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

With no annotations, the description must convey behavioral traits. It only implies a read operation without disclosing side effects, rate limits, authorization needs, or whether results are paginated. The description is too sparse to fully inform the agent.

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?

The description is a single sentence with 8 words, making it very concise. However, it could include more useful context without becoming verbose, so it is efficient but slightly under-specified.

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?

No output schema is provided, and the description does not specify what data is returned (e.g., names, IDs, hierarchy). Given the complexity of anatomical structures, this omission limits the agent's ability to decide if the tool meets its needs.

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% (both `graphId` and `numRows` have descriptions). The description adds no additional parameter semantics beyond what the schema provides, 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?

The description clearly states the tool retrieves data about anatomical structures from OntologiesApi. However, it does not differentiate from the sibling tool `get_structure_graphs`, which likely has a similar focus, leaving ambiguity about the exact data returned.

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 over alternatives. For example, it does not explain when to choose `get_structures` over `get_structure_graphs` or mention prerequisites or context for use.

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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