c3fst-mcp-server

c3fst MCP Server

MCP server for c3fst biomedical search engine.

Datasets

Source	Description	Records
products	FDA Orange Book — drug products, ingredients, manufacturers	48,502
mesh	MeSH medical subject headings — diseases, procedures, anatomy	1,011,763
variants	ClinVar genomic variants — genes, clinical significance, phenotypes	9,029,235

Tools

• search(source, query) — BM25-ranked full-text search across any dataset
• sources() — List available datasets with record counts

Remote Endpoint

This server runs remotely via SSE transport:

https://home.flamingyak.com/sse

To connect from an MCP client (Claude Desktop, Cursor, etc.), add to your MCP config:

{
  "mcpServers": {
    "c3fst": {
      "url": "https://home.flamingyak.com/sse"
    }
  }
}

Local Usage

For local development, run the server directly:

pip install mcp
python server.py

Set environment variables as needed:

• C3FST_BIN — path to c3fst binary
• C3FST_DB — path to RocksDB database
• C3MCP_TRANSPORT — stdio (default), sse, or http
• C3MCP_PORT — port for SSE/HTTP transport (default: 3000)
• C3MCP_MAX_RESULTS — max results per search (default: 20)

License

MIT