`search_experiments`

Pack: expression-atlas · Endpoint: https://gateway.pipeworx.io/expression-atlas/mcp

Search EBI Expression Atlas — ~4,500 curated gene/protein expression experiments (baseline & differential) across species, tissues, and conditions. Filter by keyword (matches description/experimental factors), species (e.g. “Homo sapiens”, “Mus musculus”), and/or type (“Baseline” or “Differential”). Returns accession, description, species, type, assay count, and factors. Keyless. Complements UniProt/Ensembl.

Parameters

Name	Type	Required	Description
`query`	string	no	Keyword matched (case-insensitive) against experiment description OR any experimental factor, e.g. “liver”, “stress”, “cancer”.
`species`	string	no	Species substring (case-insensitive), e.g. “Homo sapiens”, “Mus musculus”, “Arabidopsis thaliana”.
`type`	string	no	Experiment type: “Baseline” or “Differential”.
`limit`	number	no	Max results (default 25, max 100).

Example call

Arguments

{
  "query": "liver",
  "species": "Homo sapiens",
  "type": "Baseline",
  "limit": 25
}

curl

curl -X POST https://gateway.pipeworx.io/expression-atlas/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"search_experiments","arguments":{"query":"liver","species":"Homo sapiens","type":"Baseline","limit":25}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('search_experiments', {
  "query": "liver",
  "species": "Homo sapiens",
  "type": "Baseline",
  "limit": 25
});

More examples

{
  "query": "cancer stress",
  "type": "Differential",
  "limit": 50
}

Connect

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

{
  "mcpServers": {
    "expression-atlas": {
      "url": "https://gateway.pipeworx.io/expression-atlas/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

search_experiments