io.github.cyanheads/pubmed-mcp-server

io.github.cyanheads/pubmed-mcp-server·v2.6.6·Search

Quality Score

/100

Search PubMed, fetch articles and full text, generate citations, and explore MeSH terms via NCBI.

Repository →Remote endpoint →

§01 Install

Remote endpoint

Streamable HTTP / SSE endpoint. Add to any MCP client that supports remote servers.

https://pubmed.caseyjhand.com/mcp

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "info",
        "NCBI_API_KEY": "<ncbi_api_key>",
        "NCBI_ADMIN_EMAIL": "<ncbi_admin_email>",
        "UNPAYWALL_EMAIL": "<unpaywall_email>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_PUBLIC_URL": "<mcp_public_url>",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Cursor (.cursor/mcp.json)

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "info",
        "NCBI_API_KEY": "<ncbi_api_key>",
        "NCBI_ADMIN_EMAIL": "<ncbi_admin_email>",
        "UNPAYWALL_EMAIL": "<unpaywall_email>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_PUBLIC_URL": "<mcp_public_url>",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Cline (cline_mcp_settings.json)

npx -y @cyanheads/pubmed-mcp-server

§02 Environment variables

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'.

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.

§03 MCP Quality Score · methodology

freshness

completeness

installability

documentation

stability

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