Allen Brain Atlas

liveBiologyResearchScience

Gene expression experiments and the brain structure ontology from the Allen Institute's Brain Atlas — where in the brain a gene is expressed.

3tools
0msauth
free tier50 calls/day

Tools

allen_search_genes

Finds genes in the Allen Brain Atlas by symbol, name or Entrez ID, with the organism each record belongs to.

No parameters required.

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allen_structures

Resolves a brain region name or acronym to its Allen structure id, parent, and root-to-leaf containment path.

No parameters required.

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allen_expression_datasets

Lists the Allen Brain Atlas in-situ hybridization experiments for a gene, with atlas product and plane of section.

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/allen-brain/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/allen-brain/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"allen_search_genes","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("allen_search_genes", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("gene expression experiments and the brain structure ontology from the allen institute's brain atlas — where in the brain a gene is expressed");