A
license-
qualityC
maintenanceEnables querying ChEMBL drug discovery database for molecules, targets, activities, and drug indications. Part of Pipeworx MCP gateway.
9
MIT
expression-atlas
by pipeworx-io
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@expression-atlasshow baseline expression of BRCA1 in human breast tissue"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
mcp-expression-atlas
EBI Expression Atlas MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.
Tools
Tool | Description |
| 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. |
| 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. |
Related MCP server: mcp-opentargets
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"expression-atlas": {
"url": "https://gateway.pipeworx.io/expression-atlas/mcp"
}
}
}Or connect to the full Pipeworx gateway for access to all 1394+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Expression Atlas data" })The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
This server cannot be installed
Maintenance
–Maintainers
–Response time
–Release cycle
–Releases (12mo)
Commit activity
Resources
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Looking for Admin?
If you are the server author, to access and configure the admin panel.
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