Koskamo

pubmed-stream MCP

An open-source Python library and command-line tool that serves as a PubMed MCP server for AI assistants like Claude Code, Codex, and Gemini CLI. It enables researchers to search PubMed, download full-text articles from PubMed Central, map evidence networks, and build Obsidian knowledge graphs, allowing agents to answer research questions using only downloaded and read papers.

Package and access

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

pubmed-stream MCP logo, by melhzyCommunity listingLocal stdioSource reviewed; not executedPublished by melhzy
Vendor documentation

What you can do with it

  • Search PubMed and PubMed Central with field tags and MeSH
  • Bulk-download full-text articles from PubMed Central as JSON
  • Map evidence around a paper including citing and cited articles
  • Build a knowledge graph of a study in Obsidian

Source and maintenance

Community listingRegistry 0.4.4
mcp-registry: io.github.melhzy/pubmed-stream@0.4.4Source repositoryProject website
Maintenance checked

Packages and installation

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

pubmed-stream 0.4.4

pypiuvx
pubmed-stream package definition
{
  "version": "0.4.4",
  "transport": "stdio",
  "identifier": "pubmed-stream",
  "runtimeHint": "uvx",
  "registryType": "pypi",
  "registryBaseUrl": "https://pypi.org",
  "packageArguments": [
    {
      "type": "positional",
      "value": "mcp"
    }
  ],
  "environmentVariables": [
    {
      "name": "NCBI_API_KEY",
      "format": "string",
      "description": "Optional free NCBI API key, which raises NCBI's limit from 3 to 10 requests a second; create it under API Key Management at https://account.ncbi.nlm.nih.gov/settings/"
    },
    {
      "name": "NCBI_EMAIL",
      "format": "string",
      "description": "Optional contact email that NCBI asks programs to send with their requests"
    }
  ]
}

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.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "pubmed-stream-mcp": {
      "command": "uvx",
      "args": [
        "pubmed-stream==0.4.4",
        "mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_EMAIL": "<YOUR_NCBI_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-stream-mcp": {
      "command": "uvx",
      "args": [
        "pubmed-stream==0.4.4",
        "mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_EMAIL": "<YOUR_NCBI_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-stream-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "pubmed-stream==0.4.4",
        "mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_EMAIL": "<YOUR_NCBI_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-stream-mcp": {
      "command": "uvx",
      "args": [
        "pubmed-stream==0.4.4",
        "mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "NCBI_EMAIL": "<YOUR_NCBI_EMAIL>"
      }
    }
  }
}

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