`allen_search_genes`

Pack: allen-brain · Endpoint: https://gateway.pipeworx.io/allen-brain/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/allen_search_genes for the schema, then POST the same URL with its arguments for the data.

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

Tool description as the model sees it

Look up genes in the Allen Brain Atlas gene catalog by symbol/acronym, name substring, or Entrez ID. AUTHORITATIVE for resolving a gene to the Allen internal gene id and organism that the atlas expression data is keyed on — note the atlas holds mouse and human as SEPARATE gene records with the same-but-differently-cased acronym (Gabra1 vs GABRA1), and the expression datasets attached to each differ. Use this before allen_expression_datasets.

Parameters

Name	Type	Required	Description
`acronym`	string	no	Exact gene symbol, e.g. “Gabra1” (mouse) or “GABRA1” (human). Case matters for the exact match; matching is retried case-insensitively and the response says which casing hit.
`name_contains`	string	no	Substring of the gene name, e.g. “dopamine receptor”. Case-insensitive.
`entrez_id`	number	no	NCBI Entrez Gene ID, e.g. 14394.
`organism`	string	no	Filter results to “mouse”, “human”, or omit for both.
`num_rows`	number	no	Rows to return, 1-200 (default 25).
`start_row`	number	no	0-based offset for paging (default 0).

Example call

Arguments

{
  "acronym": "Gabra1"
}

curl

curl -X POST https://gateway.pipeworx.io/allen-brain/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"allen_search_genes","arguments":{"acronym":"Gabra1"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('allen_search_genes', {
  "acronym": "Gabra1"
});

More examples

{
  "name_contains": "dopamine receptor",
  "organism": "human"
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "allen-brain": {
      "url": "https://gateway.pipeworx.io/allen-brain/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

allen_search_genes