PubMed MCP Server

Name: PubMed MCP Server
Author: cyanheads

cyanheads

Get started Repository Website & docs

Search PubMed and Europe PMC, fetch articles and full text, citations and MeSH terms.

Setup

Choose your client, copy the config, then fill in any required environment variables.

Add to Cursor Add to VS Code

Local

claude mcp add pubmed --env MCP_TRANSPORT_TYPE='<MCP_TRANSPORT_TYPE>' --env MCP_LOG_LEVEL='<MCP_LOG_LEVEL>' --env NCBI_API_KEY='<NCBI_API_KEY>' -- npx -y @cyanheads/pubmed-mcp-server

~/.codex/config.toml

[mcp_servers.pubmed]
command = "npx"
args = ["-y", "@cyanheads/pubmed-mcp-server"]
env = { MCP_TRANSPORT_TYPE = "<MCP_TRANSPORT_TYPE>", MCP_LOG_LEVEL = "<MCP_LOG_LEVEL>", NCBI_API_KEY = "<NCBI_API_KEY>" }

# codex mcp add pubmed --env MCP_TRANSPORT_TYPE='<MCP_TRANSPORT_TYPE>' --env MCP_LOG_LEVEL='<MCP_LOG_LEVEL>' --env NCBI_API_KEY='<NCBI_API_KEY>' -- npx -y @cyanheads/pubmed-mcp-server

~/.cursor/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<MCP_TRANSPORT_TYPE>",
        "MCP_LOG_LEVEL": "<MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<NCBI_API_KEY>"
      }
    }
  }
}

.vscode/mcp.json

{
  "servers": {
    "pubmed": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<MCP_TRANSPORT_TYPE>",
        "MCP_LOG_LEVEL": "<MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<NCBI_API_KEY>"
      }
    }
  }
}

~/.gemini/settings.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<MCP_TRANSPORT_TYPE>",
        "MCP_LOG_LEVEL": "<MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<NCBI_API_KEY>"
      }
    }
  }
}

claude_desktop_config.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<MCP_TRANSPORT_TYPE>",
        "MCP_LOG_LEVEL": "<MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<NCBI_API_KEY>"
      }
    }
  }
}

.trae/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubmed-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<MCP_TRANSPORT_TYPE>",
        "MCP_LOG_LEVEL": "<MCP_LOG_LEVEL>",
        "NCBI_API_KEY": "<NCBI_API_KEY>"
      }
    }
  }
}

Remote

claude mcp add --transport http pubmed https://pubmed.caseyjhand.com/mcp

~/.codex/config.toml

[mcp_servers.pubmed]
url = "https://pubmed.caseyjhand.com/mcp"

# codex mcp add pubmed --url https://pubmed.caseyjhand.com/mcp

~/.cursor/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

.vscode/mcp.json

{
  "servers": {
    "pubmed": {
      "type": "http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

~/.gemini/settings.json

{
  "mcpServers": {
    "pubmed": {
      "httpUrl": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

claude_desktop_config.json · Customize › Connectors › Add custom connector

{
  "mcpServers": {
    "pubmed": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://pubmed.caseyjhand.com/mcp"
      ]
    }
  }
}

.trae/mcp.json

{
  "mcpServers": {
    "pubmed": {
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

Environment variables

MCP_TRANSPORT_TYPE
MCP_LOG_LEVEL
NCBI_API_KEY

Replace the placeholders with your own credentials and keep them out of version control.

Setup

Local

Remote

Environment variables

Related