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mcp/harbor

Gemini CLI pubmed mcp server pubmed_format_citations

How to: Gemini CLI pubmed mcp server pubmed_format_citations

client:Gemini CLI transport:streamable-http tool:pubmed_format_citations

Add pubmed mcp server to Gemini CLI

  1. 01

    Open ~/.gemini/settings.json and merge this in. Keep any servers already there. 

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "httpUrl": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}
  1. 02

    Save the file and restart Gemini CLI.

  2. 03

    Ask for something pubmed_format_citations does. Gemini CLI lists the server's tools on connect and calls pubmed_format_citations itself — you do not invoke it by name.

  3. 04

    If nothing happens, check the server is running and that pubmed mcp server's identifier in your config matches the one above exactly.

Gemini expands $VAR and ${VAR} inside env values, so a secret can live in your shell rather than this file. Gemini CLI docs

Set these first

pubmed mcp server will not start until these are set, so pubmed_format_citations never becomes available.

  • MCP_LOG_LEVEL
  • NCBI_API_KEY
  • NCBI_ADMIN_EMAIL
  • UNPAYWALL_EMAIL

Same tool, other clients

This list was read from the server itself, by connecting to it and calling tools/list on 24 September 2026. It is what the server actually exposes, not what its listing claims.

Mutating and Read-only are read off each tool's name, not its schema — a hint, not a guarantee. The registry stores tool names only; connect the server for its live schemas.

pubmed mcp server MCP server