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Allen Structures

allen_structures
Read-onlyIdempotent

Query the Allen Brain Atlas structure ontology — the canonical hierarchy of named brain regions (Field CA1, Primary visual area, Substantia nigra) with their acronyms, colors, parent structure, and full root-to-leaf structure_id_path. AUTHORITATIVE for resolving a brain-region name or acronym to the structure ID that Allen expression, connectivity and reference-space data are annotated against, and for establishing whether one region contains another.

Input Schema

NameRequiredDescriptionDefault
acronymNoExact structure acronym, e.g. "CA1", "VISp", "SNr".
graph_idNoStructure graph to search. 1 = adult mouse brain (default), 10 = human brain, 17 = developing mouse.
num_rowsNoRows to return, 1-200 (default 25).
start_rowNo0-based offset for paging (default 0).
structure_idNoAllen structure id, e.g. 382 (Field CA1).
name_containsNoSubstring of the structure name, e.g. "hippocamp", "visual area". Case-insensitive.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already declare the safe read-only, idempotent, non-destructive profile, so the bar is lower. The description adds real domain behavior beyond them: this is the canonical/authoritative hierarchy, it supports containment reasoning, and the returned fields are enumerated. It does not discuss default result size when no filter is supplied, but that is covered by schema defaults.

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?

Two sentences, front-loaded with what the tool returns and followed by the authoritative-use case; nothing is redundant with the schema. The sentences are dense and long, which slightly reduces scannability but every clause carries information.

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 correctly compensates by listing the fields returned (acronym, color, parent, structure_id_path). All six parameters are schema-documented and none are required, matching the multi-filter design. It leaves open what a filterless call returns (full ontology vs. default 25 rows) and result ordering, a minor gap.

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% and every parameter is documented with examples, so the baseline is 3. The description adds the resolution relationship between name/acronym and structure_id and the notion of a root-to-leaf structure_id_path, but no filter-combination or matching semantics beyond what the schema already states.

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

Purpose5/5

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

Specific verb+resource ('Query the Allen Brain Atlas structure ontology') with the exact content of the resource enumerated (acronyms, colors, parent structure, structure_id_path). It also differentiates from siblings by naming itself AUTHORITATIVE for resolving names/acronyms to structure IDs used by Allen expression, connectivity, and reference-space data, so an agent can distinguish it from allen_expression_datasets and allen_search_genes.

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

Usage Guidelines4/5

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

Gives clear when-to-use conditions: resolving a brain-region name or acronym to the structure ID that other Allen data is annotated against, and establishing containment between regions. No explicit exclusions or named alternatives (e.g., 'for gene lookup use allen_search_genes') are given, so it stops short of full routing guidance.

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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