Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation
Config is the same across clients — only the file and path differ.
{
"mcpServers": {
"ensembl": {
"url": "https://gateway.pipeworx.io/ensembl/mcp"
}
}
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Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
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Ensembl REST MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
| 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. |
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"
}
}
}
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.
MIT