Allen Brain API MCP Server

list_well_known_files

Discover downloadable files attached to Allen brain resources. Specify resource ID and optional filters to retrieve transcriptomics matrices, reference data, and more.

Instructions

List downloadable files (WellKnownFiles) attached to any Allen resource such as a Product, Specimen, or SectionDataSet. Use this to discover transcriptomics matrices, reference data, or other bulk downloads.

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": {
      "attachableId": "<attachableId>"
    },
    "name": "list_well_known_files"
  }
}

Input Schema

Name	Required	Description
`attachableId`	Yes	ID of the resource to look up files for (e.g. a Product ID or Specimen ID).
`attachableType`	No	Type of the resource, e.g. 'Product', 'Specimen', 'SectionDataSet'. Omit to search across all types.
`wellKnownFileTypeName`	No	Filter by file type name, e.g. 'RNASeqSummarizedToGenesAsCSV', '3DNeuronReconstruction', 'NWBDownload'.
`numRows`	No	Maximum number of rows to return (default is 50).

Schema Changelog

Changes observed during successful MCP inspections.

First observedv1.0.0May 29, 2026

TDQS

A3.5/5.0

Behavior2/5

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

No annotations are provided, so the description bears full burden. It states the tool 'lists' files but omits details like read-only nature, pagination, ordering, authentication requirements, or rate limits, which are important for safe invocation.

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 two concise sentences, front-loading the core action and providing immediate context without unnecessary words.

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

Completeness3/5

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

The tool has 4 parameters (1 required) with clear schema descriptions. However, there is no output schema, and the description does not hint at what the list contains (e.g., file names, IDs, download URLs), leaving a gap in completeness.

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%, so baseline is 3. The description adds examples for wellKnownFileTypeName but does not provide additional semantic meaning beyond the schema's descriptions for attachableType or numRows.

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?

The description clearly states the tool lists 'WellKnownFiles' attached to specific resource types like Product, Specimen, or SectionDataSet, and gives examples of file types such as transcriptomics matrices. This distinguishes it from siblings like download_well_known_file.

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

Usage Guidelines3/5

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

The description says 'Use this to discover transcriptomics matrices, reference data, or other bulk downloads,' providing context on when to use it. However, it does not mention when not to use it or compare to alternatives like download_well_known_file.

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