Expression Atlas

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EBI Expression Atlas — search and retrieve metadata for ~4,500 curated gene/protein expression experiments across species and tissues.

2 tools
0ms auth
free tier 50 calls/day

Tools

search_experiments

Search EBI Expression Atlas — ~4,500 curated gene/protein expression experiments (baseline & differential) across species, tissues, and conditions. Filter by keyword (matches description/experimental

No parameters required.

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get_experiment

Get metadata for a single EBI Expression Atlas experiment by accession (e.g. "E-MTAB-4045"). Returns accession, description, species, type, assay count, and experimental factors.

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/expression-atlas/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/expression-atlas/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"search_experiments","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("search_experiments", {});
ask_pipeworx 
// Or ask in plain English:
const answer = await px.ask("ebi expression atlas — search and retrieve metadata for ~4,500 curated gene/protein expression experiments across species and tissues");