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mcp/harbor

Gemini CLI pubmed mcp server Prompt/research_plan

How to: Gemini CLI pubmed mcp server research_plan

client:Gemini CLI transport:streamable-http prompt:research_plan

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

    research_plan is surfaced in the client's prompt or command menu. Unlike a tool, you invoke it deliberately — Gemini CLI will not call it for you.

  3. 04

    If it does not appear, check that pubmed mcp server is connected and that you are looking at its prompts rather than its tools.

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 it never reaches Gemini CLI.

  • MCP_LOG_LEVEL
  • NCBI_API_KEY
  • NCBI_ADMIN_EMAIL
  • UNPAYWALL_EMAIL

Same prompt, other clients

Read from the server itself, by connecting to it and calling prompts/list on 24 September 2026. A listing does not declare its prompts, so asking is the only way to know them, and this is what the server actually offers rather than what its listing claims. Names only are stored; connect the server for each prompt's arguments.

pubmed mcp server MCP server