io.github.cyanheads/pubmed-mcp-server MCP Server

Name: io.github.cyanheads/pubmed-mcp-server MCP Server
Author: io.github.cyanheads

io.github.cyanheads/pubmed-mcp-server

Repository Registry

What is the io.github.cyanheads/pubmed-mcp-server MCP server?

Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.

How to install io.github.cyanheads/pubmed-mcp-server

Copy-paste configuration for popular MCP clients.

transport: stdio

Config generated by PluginBench — verify against the source before use.

Environment / auth

MCP_LOG_LEVEL
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').
NCBI_API_KEY
NCBI API key for higher rate limits (10 req/s vs 3 req/s).
NCBI_ADMIN_EMAIL
Contact email sent with NCBI requests (recommended by NCBI).
UNPAYWALL_EMAIL
Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC.
MCP_HTTP_HOST
The hostname for the HTTP server.
MCP_HTTP_PORT
The port to run the HTTP server on.
MCP_HTTP_ENDPOINT_PATH
The endpoint path for the MCP server.
MCP_PUBLIC_URL
Public origin override for deployments behind a TLS-terminating reverse proxy (e.g. https://mcp.example.com).
MCP_AUTH_MODE
Authentication mode to use: 'none', 'jwt', or 'oauth'.

Claude Desktop

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "bun",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_ADMIN_EMAIL": "<YOUR_NCBI_ADMIN_EMAIL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>",
        "MCP_HTTP_HOST": "<YOUR_MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<YOUR_MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<YOUR_MCP_HTTP_ENDPOINT_PATH>",
        "MCP_PUBLIC_URL": "<YOUR_MCP_PUBLIC_URL>",
        "MCP_AUTH_MODE": "<YOUR_MCP_AUTH_MODE>"
      }
    }
  }
}

Cursor

~/.cursor/mcp.json

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "bun",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_ADMIN_EMAIL": "<YOUR_NCBI_ADMIN_EMAIL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>",
        "MCP_HTTP_HOST": "<YOUR_MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<YOUR_MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<YOUR_MCP_HTTP_ENDPOINT_PATH>",
        "MCP_PUBLIC_URL": "<YOUR_MCP_PUBLIC_URL>",
        "MCP_AUTH_MODE": "<YOUR_MCP_AUTH_MODE>"
      }
    }
  }
}

Windsurf

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "bun",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_ADMIN_EMAIL": "<YOUR_NCBI_ADMIN_EMAIL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>",
        "MCP_HTTP_HOST": "<YOUR_MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<YOUR_MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<YOUR_MCP_HTTP_ENDPOINT_PATH>",
        "MCP_PUBLIC_URL": "<YOUR_MCP_PUBLIC_URL>",
        "MCP_AUTH_MODE": "<YOUR_MCP_AUTH_MODE>"
      }
    }
  }
}

VS Code

.vscode/mcp.json

{
  "servers": {
    "pubmed-mcp-server": {
      "type": "stdio",
      "command": "bun",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_ADMIN_EMAIL": "<YOUR_NCBI_ADMIN_EMAIL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>",
        "MCP_HTTP_HOST": "<YOUR_MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<YOUR_MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<YOUR_MCP_HTTP_ENDPOINT_PATH>",
        "MCP_PUBLIC_URL": "<YOUR_MCP_PUBLIC_URL>",
        "MCP_AUTH_MODE": "<YOUR_MCP_AUTH_MODE>"
      }
    }
  }
}

Claude Code

claude mcp add pubmed-mcp-server --env MCP_LOG_LEVEL=<YOUR_MCP_LOG_LEVEL> --env NCBI_API_KEY=<YOUR_NCBI_API_KEY> --env NCBI_ADMIN_EMAIL=<YOUR_NCBI_ADMIN_EMAIL> --env UNPAYWALL_EMAIL=<YOUR_UNPAYWALL_EMAIL> --env MCP_HTTP_HOST=<YOUR_MCP_HTTP_HOST> --env MCP_HTTP_PORT=<YOUR_MCP_HTTP_PORT> --env MCP_HTTP_ENDPOINT_PATH=<YOUR_MCP_HTTP_ENDPOINT_PATH> --env MCP_PUBLIC_URL=<YOUR_MCP_PUBLIC_URL> --env MCP_AUTH_MODE=<YOUR_MCP_AUTH_MODE> -- bun -y @cyanheads/pubmed-mcp-server run start:stdio