Data Aggregator MCP Server

io.github.musharna/data-aggregator-mcp

Repository Registry

What is the Data Aggregator MCP server?

Find & fetch research datasets across 17 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).
DATA_GOV_API_KEY
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
Email address sent to the Unpaywall API; required to enable the Unpaywall PDF fallback leg of literature full-text retrieval.
NCBI_EMAIL
Contact address sent to NCBI's ID converter; falls back to UNPAYWALL_EMAIL when unset.
DATAVERSE_BASE_URL
Resolve Dataverse DOIs against a different installation (default: https://dataverse.harvard.edu).
CACHE_TTL_SECONDS
Resolve-cache lifetime in seconds (default: 3600); an unparseable value falls back to the default.

~/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>",
        "DATA_GOV_API_KEY": "<YOUR_DATA_GOV_API_KEY>",
        "UNPAYWALL_EMAIL": "<YOUR_UNPAYWALL_EMAIL>",
        "NCBI_EMAIL": "<YOUR_NCBI_EMAIL>",
        "DATAVERSE_BASE_URL": "<YOUR_DATAVERSE_BASE_URL>",
        "CACHE_TTL_SECONDS": "<YOUR_CACHE_TTL_SECONDS>"
      }
    }
  }
}

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