Summary
Connects Claude to the Ensembl REST API for working with vertebrate genome data. Exposes seven core tools: stable ID lookups for genes, transcripts, and exons; gene symbol searches; cross-reference retrieval; sequence fetching; homology mappings; variation records; and the Variant Effect Predictor for analyzing genomic regions. Part of the Pipeworx gateway ecosystem, so you can either connect to just Ensembl or get access to their full catalog of 250+ data sources through a single endpoint. Useful when you need to annotate variants, trace gene homologs across species, or pull reference sequences without writing REST client code yourself.
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mcp-ensembl
Ensembl REST MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
Tools
| Tool | Description |
|---|---|
lookup | Lookup by stable id (gene/transcript/exon/translation). |
lookup_symbol | Gene by symbol within a species. |
xrefs | External cross-references for a gene symbol. |
sequence | Sequence by stable id. |
homology | Homology mappings for a gene. |
variation | Variation record by name. |
vep | Variant Effect Predictor — region in "chrom:start-end:strand" form. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"ensembl": {
"url": "https://gateway.pipeworx.io/ensembl/mcp"
}
}
}
Or connect to the full Pipeworx gateway for access to all 673+ 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 Ensembl data" })
The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
Featured
Keep your Mac awake while Claude Code and 40+ AI agents run. Sleeps when they're idle.
One time payment $9 →Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →On Capafy, your Skill runs online 24/7 as an agent product, and you get paid every time someone uses it.
Start earning →