MCP Server

Data Aggregator MCP Server

Name: Data Aggregator MCP Server
Author: io.github.musharna

io.github.musharna/data-aggregator-mcp

Repository Registry

What is the Data Aggregator MCP server?

Find & fetch research datasets across 12 archives, omics registries, and literature sources.

How to install Data Aggregator

Copy-paste configuration for popular MCP clients.

transport: stdio

Config generated by PluginBench — verify against the source before use.

Environment / auth

NCBI_API_KEY
secret
Optional NCBI E-utilities API key; raises the rate limit 3->10 req/s for omics, literature, and taxonomy lookups.
LLM_API_BASE
Base URL of an OpenAI-compatible /chat/completions endpoint; enables search(understand=true) and search(multi_query=true).
LLM_API_KEY
secret
Bearer token for the LLM endpoint (LLM_API_BASE); omit for keyless local servers.
LLM_MODEL
Model name passed to the LLM endpoint (default: gpt-4o-mini); set to whatever your endpoint serves.
EMBEDDING_API_BASE
Base URL of an OpenAI-compatible /embeddings endpoint; enables search(rank=semantic) re-ranking.
EMBEDDING_API_KEY
secret
Bearer token for the embeddings endpoint (EMBEDDING_API_BASE); omit for keyless local servers.
EMBEDDING_MODEL
Model name passed to the embeddings endpoint (default: text-embedding-3-small).
UNPAYWALL_EMAIL
Email address sent to the Unpaywall API; required to enable the Unpaywall PDF fallback leg of literature full-text retrieval.

Claude Desktop

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "LLM_API_BASE": "<YOUR_LLM_API_BASE>",
        "LLM_API_KEY": "<YOUR_LLM_API_KEY>",
        "LLM_MODEL": "<YOUR_LLM_MODEL>",
        "EMBEDDING_API_BASE": "<YOUR_EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<YOUR_EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<YOUR_EMBEDDING_MODEL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>"
      }
    }
  }
}

Cursor

~/.cursor/mcp.json

{
  "mcpServers": {
    "data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "LLM_API_BASE": "<YOUR_LLM_API_BASE>",
        "LLM_API_KEY": "<YOUR_LLM_API_KEY>",
        "LLM_MODEL": "<YOUR_LLM_MODEL>",
        "EMBEDDING_API_BASE": "<YOUR_EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<YOUR_EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<YOUR_EMBEDDING_MODEL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>"
      }
    }
  }
}

Windsurf

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "LLM_API_BASE": "<YOUR_LLM_API_BASE>",
        "LLM_API_KEY": "<YOUR_LLM_API_KEY>",
        "LLM_MODEL": "<YOUR_LLM_MODEL>",
        "EMBEDDING_API_BASE": "<YOUR_EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<YOUR_EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<YOUR_EMBEDDING_MODEL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>"
      }
    }
  }
}

VS Code

.vscode/mcp.json

{
  "servers": {
    "data-aggregator-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "<YOUR_NCBI_API_KEY>",
        "LLM_API_BASE": "<YOUR_LLM_API_BASE>",
        "LLM_API_KEY": "<YOUR_LLM_API_KEY>",
        "LLM_MODEL": "<YOUR_LLM_MODEL>",
        "EMBEDDING_API_BASE": "<YOUR_EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<YOUR_EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<YOUR_EMBEDDING_MODEL>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>"
      }
    }
  }
}

Claude Code

claude mcp add data-aggregator-mcp --env NCBI_API_KEY=<YOUR_NCBI_API_KEY> --env LLM_API_BASE=<YOUR_LLM_API_BASE> --env LLM_API_KEY=<YOUR_LLM_API_KEY> --env LLM_MODEL=<YOUR_LLM_MODEL> --env EMBEDDING_API_BASE=<YOUR_EMBEDDING_API_BASE> --env EMBEDDING_API_KEY=<YOUR_EMBEDDING_API_KEY> --env EMBEDDING_MODEL=<YOUR_EMBEDDING_MODEL> --env UNPAYWALL_EMAIL=<YOUR_UNPAYWALL_EMAIL> -- uvx data-aggregator-mcp

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