{
  "markdown": "# mcp-kegg\n\nKEGG REST MCP — Kyoto Encyclopedia of Genes and Genomes.\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| `find` | Search KEGG by keyword. KEGG is the authoritative bioinformatics database for compounds, drugs, diseases, metabolic pathways, genes, and enzymes. Pick a database (compound\\|drug\\|disease\\|pathway\\|genes\\|enzyme\\|glycan\\|module\\|ko) and pass a query like \"glucose\", \"aspirin\", or \"diabetes\". Returns matching KEGG IDs with descriptions. Keyless. |\n| `get_entry` | Fetch a full KEGG flat-file entry by ID and return it as parsed fields plus raw text. IDs look like \"C00031\" (compound), \"hsa00010\" (pathway), \"D00009\" (drug), \"K00844\" (KO/ortholog), or \"ec:1.1.1.1\" (enzyme). Parsed fields include ENTRY, NAME, FORMULA, CLASS, PATHWAY, DESCRIPTION, cross-references, and more. Use find first to discover IDs. Keyless. |\n| `list_database` | List all entries in a KEGG database (id + description). Useful for enumerating things like KEGG pathways (\"pathway\"), drugs (\"drug\"), or supported organisms (\"organism\"). Results are capped at 100 with a truncated flag. Keyless. |\n\n## Quick Start\n\nAdd to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):\n\n```json\n{\n  \"mcpServers\": {\n    \"kegg\": {\n      \"url\": \"https://gateway.pipeworx.io/kegg/mcp\"\n    }\n  }\n}\n```\n\n### What this endpoint actually serves\n\n`tools/list` at `https://gateway.pipeworx.io/kegg/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 Kegg 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-kegg",
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