{
  "markdown": "# mcp-rhea\n\nRhea MCP — expert-curated database of biochemical reactions.\n\nPart of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 1476+ live data sources.\n\n## Tools\n\n| Tool | Description |\n|------|-------------|\n| `search_reactions` | Search Rhea, the expert-curated database of biochemical reactions (the reaction reference used by UniProt and KEGG). Find enzyme/metabolic reactions by compound name, ChEBI id, EC number, or keyword and get the balanced plain-text reaction equation plus EC and ChEBI cross-references. Keyless. |\n| `get_reaction` | Fetch a single Rhea reaction by its Rhea id (e.g. \"RHEA:14293\" or \"14293\"). Returns the balanced plain-text equation plus EC number, ChEBI compound, UniProt enzyme and PubMed cross-references. Rhea is the expert-curated biochemical reaction reference used by UniProt and KEGG. Keyless. |\n\n## Quick Start\n\nAdd to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):\n\n```json\n{\n  \"mcpServers\": {\n    \"rhea\": {\n      \"url\": \"https://gateway.pipeworx.io/rhea/mcp\"\n    }\n  }\n}\n```\n\n### What this endpoint actually serves\n\n`tools/list` at `https://gateway.pipeworx.io/rhea/mcp` returns the tools in the table\nabove **plus the shared Pipeworx meta-tools** — `ask_pipeworx`,\n`discover_tools`, `search_within`, `remember`/`recall` and the rest of the\ngateway-wide set. So the tool count you see is larger than this table: a\nsingle-pack endpoint currently lists roughly 30 shared tools alongside the\npack's own. The connection's `initialize` response states its exact scope, and\nis the authoritative answer for a given day.\n\nThis is deliberate, not multiplexing by accident. The meta-tools are what let a\nscoped connection answer a question this pack does not cover — via\n`ask_pipeworx`, which routes across the whole catalog — without you adding a\nsecond MCP server. There is currently no way to mount a pack endpoint without\nthem; if the extra schemas cost you more context than the routing is worth,\nconnect to the full gateway once rather than to several pack endpoints.\n\nOr connect to the full Pipeworx gateway to get every pack's tools listed\ndirectly, instead of just this one's:\n\n```json\n{\n  \"mcpServers\": {\n    \"pipeworx\": {\n      \"url\": \"https://gateway.pipeworx.io/mcp\"\n    }\n  }\n}\n```\n\nBoth URLs reach the same gateway and the same 1476+ data sources. The\nonly difference is which pack's tools are listed **directly**; `ask_pipeworx`\nreaches all of them from either one.\n\n## Using with ask_pipeworx\n\nInstead of calling tools directly, you can ask questions in plain English —\nthis works on the pack endpoint above as well as on the full gateway:\n\n```\nask_pipeworx({ question: \"your question about Rhea data\" })\n```\n\nThe gateway picks the right tool and fills the arguments automatically.\n\n## More\n\n- [Docs and guides](https://pipeworx.io/docs)\n- [pipeworx.io](https://pipeworx.io)\n\n## License\n\nMIT\n",
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  "repo_slug": "pipeworx-io/mcp-rhea",
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