pubmed-mcp-server

A community-driven MCP server that enables agents to search PubMed and Europe PMC, fetch article metadata and full text, retrieve citation metrics, format references, and look up MeSH terms. It supports STDIO and Streamable HTTP transports.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by cyanheads

Vendor documentation

What you can do with it

Search PubMed with full query syntax and structured filters
Fetch article metadata and full text by PMID, PMCID, or DOI
Look up MeSH headings with tree numbers and scope notes
Format citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver

Source and maintenance

Community listingRegistry 2.11.1

mcp-registry: io.github.cyanheads/pubmed-mcp-server@2.11.1 Source repository

Maintenance checked: Oct 31, 2026, 10:59 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@cyanheads/pubmed-mcp-server 2.11.1

npmnpx

@cyanheads/pubmed-mcp-server package definition

{
  "version": "2.11.1",
  "transport": "stdio",
  "identifier": "@cyanheads/pubmed-mcp-server",
  "runtimeHint": "npx",
  "registryType": "npm",
  "registryBaseUrl": "https://registry.npmjs.org",
  "environmentVariables": [
    {
      "name": "MCP_LOG_LEVEL",
      "format": "string",
      "default": "info",
      "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
    },
    {
      "name": "NCBI_API_KEY",
      "format": "string",
      "description": "NCBI API key for higher rate limits (10 req/s vs 3 req/s)."
    },
    {
      "name": "NCBI_ADMIN_EMAIL",
      "format": "string",
      "description": "Contact email sent with NCBI requests (recommended by NCBI)."
    },
    {
      "name": "UNPAYWALL_EMAIL",
      "format": "string",
      "description": "Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server@2.11.1"
      ],
      "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>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server@2.11.1"
      ],
      "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>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "pubmed-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server@2.11.1"
      ],
      "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>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server@2.11.1"
      ],
      "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>"
      }
    }
  }
}

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