Summary
Connects Claude to the Reactome pathway database, exposing five tools for querying biological pathways and molecular interactions. You can search across all objects, pull full pathway records by stable ID, list entity participants, find pathways containing specific proteins via UniProt accessions, and query orthologous events across species. Runs through Pipeworx's gateway infrastructure, which offers both a standalone Reactome endpoint and a unified gateway to 673+ data sources. Useful when you need structured pathway data during research or when building biological analysis workflows. Supports plain English queries through ask_pipeworx instead of direct tool calls.
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mcp-reactome
Reactome MCP — open biological pathway knowledge-base.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
Tools
| Tool | Description |
|---|---|
search | Search across all Reactome objects. |
pathway | Full pathway record by stable id (e.g. R-HSA-68886). |
participants | Entity participants of a pathway. |
pathways_for_entity | Pathways containing an entity, looked up by external resource id (e.g. UniProt accession). |
orthologous_events | Orthologous pathways/reactions in another species. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"reactome": {
"url": "https://gateway.pipeworx.io/reactome/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 Reactome 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 →
