Data Aggregator

io.github.musharna/data-aggregator-mcp · v0.76.0

Find & fetch research datasets across 21 archives, omics registries, and literature sources.

Source code Set it up

Connect Runs on your machine

Terminal

claude mcp add data-aggregator-mcp -e NCBI_API_KEY=<NCBI_API_KEY> -e LLM_API_BASE=<LLM_API_BASE> -e LLM_API_KEY=<LLM_API_KEY> -e LLM_MODEL=<LLM_MODEL> -e EMBEDDING_API_BASE=<EMBEDDING_API_BASE> -e EMBEDDING_API_KEY=<EMBEDDING_API_KEY> -e EMBEDDING_MODEL=<EMBEDDING_MODEL> -e DATA_GOV_API_KEY=<DATA_GOV_API_KEY> -e UNPAYWALL_EMAIL=<UNPAYWALL_EMAIL> -e NCBI_EMAIL=<NCBI_EMAIL> -e DATAVERSE_BASE_URL=<DATAVERSE_BASE_URL> -e CACHE_TTL_SECONDS=<CACHE_TTL_SECONDS> -- uvx data-aggregator-mcp==0.76.0

claude_desktop_config.json

{
  "mcpServers": {
    "data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp==0.76.0"
      ],
      "env": {
        "NCBI_API_KEY": "<NCBI_API_KEY>",
        "LLM_API_BASE": "<LLM_API_BASE>",
        "LLM_API_KEY": "<LLM_API_KEY>",
        "LLM_MODEL": "<LLM_MODEL>",
        "EMBEDDING_API_BASE": "<EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<EMBEDDING_MODEL>",
        "DATA_GOV_API_KEY": "<DATA_GOV_API_KEY>",
        "UNPAYWALL_EMAIL": "<UNPAYWALL_EMAIL>",
        "NCBI_EMAIL": "<NCBI_EMAIL>",
        "DATAVERSE_BASE_URL": "<DATAVERSE_BASE_URL>",
        "CACHE_TTL_SECONDS": "<CACHE_TTL_SECONDS>"
      }
    }
  }
}

~/.cursor/mcp.json

{
  "mcpServers": {
    "data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp==0.76.0"
      ],
      "env": {
        "NCBI_API_KEY": "<NCBI_API_KEY>",
        "LLM_API_BASE": "<LLM_API_BASE>",
        "LLM_API_KEY": "<LLM_API_KEY>",
        "LLM_MODEL": "<LLM_MODEL>",
        "EMBEDDING_API_BASE": "<EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<EMBEDDING_MODEL>",
        "DATA_GOV_API_KEY": "<DATA_GOV_API_KEY>",
        "UNPAYWALL_EMAIL": "<UNPAYWALL_EMAIL>",
        "NCBI_EMAIL": "<NCBI_EMAIL>",
        "DATAVERSE_BASE_URL": "<DATAVERSE_BASE_URL>",
        "CACHE_TTL_SECONDS": "<CACHE_TTL_SECONDS>"
      }
    }
  }
}

.vscode/mcp.json

{
  "servers": {
    "data-aggregator-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "data-aggregator-mcp==0.76.0"
      ],
      "env": {
        "NCBI_API_KEY": "<NCBI_API_KEY>",
        "LLM_API_BASE": "<LLM_API_BASE>",
        "LLM_API_KEY": "<LLM_API_KEY>",
        "LLM_MODEL": "<LLM_MODEL>",
        "EMBEDDING_API_BASE": "<EMBEDDING_API_BASE>",
        "EMBEDDING_API_KEY": "<EMBEDDING_API_KEY>",
        "EMBEDDING_MODEL": "<EMBEDDING_MODEL>",
        "DATA_GOV_API_KEY": "<DATA_GOV_API_KEY>",
        "UNPAYWALL_EMAIL": "<UNPAYWALL_EMAIL>",
        "NCBI_EMAIL": "<NCBI_EMAIL>",
        "DATAVERSE_BASE_URL": "<DATAVERSE_BASE_URL>",
        "CACHE_TTL_SECONDS": "<CACHE_TTL_SECONDS>"
      }
    }
  }
}

Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.

Tools

This server runs locally, so its tools are listed by your MCP client once it starts.

Environment variables

Name	Description
`NCBI_API_KEY` Optional, secret	Optional NCBI E-utilities API key; raises the rate limit 3->10 req/s for omics, literature, and taxonomy lookups.
`LLM_API_BASE` Optional	Base URL of an OpenAI-compatible /chat/completions endpoint; enables search(understand=true) and search(multi_query=true).
`LLM_API_KEY` Optional, secret	Bearer token for the LLM endpoint (LLM_API_BASE); omit for keyless local servers.
`LLM_MODEL` Optional	Model name passed to the LLM endpoint (default: gpt-4o-mini); set to whatever your endpoint serves.
`EMBEDDING_API_BASE` Optional	Base URL of an OpenAI-compatible /embeddings endpoint; enables search(rank=semantic) re-ranking.
`EMBEDDING_API_KEY` Optional, secret	Bearer token for the embeddings endpoint (EMBEDDING_API_BASE); omit for keyless local servers.
`EMBEDDING_MODEL` Optional	Model name passed to the embeddings endpoint (default: text-embedding-3-small).
`DATA_GOV_API_KEY` Optional, secret	Optional api.data.gov key for the data.gov source; without it requests fall back to the shared public DEMO_KEY, which is aggressively rate-limited.
`UNPAYWALL_EMAIL` Optional	Email address sent to the Unpaywall API; required to enable the Unpaywall PDF fallback leg of literature full-text retrieval.
`NCBI_EMAIL` Optional	Contact address sent to NCBI's ID converter; falls back to UNPAYWALL_EMAIL when unset.
`DATAVERSE_BASE_URL` Optional	Resolve Dataverse DOIs against a different installation (default: https://dataverse.harvard.edu).
`CACHE_TTL_SECONDS` Optional	Resolve-cache lifetime in seconds (default: 3600); an unparseable value falls back to the default.

Details

Package	`[email protected]` (PYPI, stdio)
First published	13 Nov 2026
Last updated	13 Nov 2026
Registry name	`io.github.musharna/data-aggregator-mcp`

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Local install

Installed and run on your own machine, so there is no public endpoint to check.

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