Data Aggregator MCP Server

Find & fetch research datasets across Zenodo, DataCite, NCBI omics, and literature.

Remote serverstreamable-httpPython

What is the Data Aggregator MCP Server?

Find & fetch research datasets across Zenodo, DataCite, NCBI omics, and literature.

The short version

search one query across 17 sources — Zenodo, DataCite (Dryad / Figshare / Dataverse / OSF / OpenNeuro / Mendeley), NCBI omics (GEO / SRA / BioProject), BioStudies (EBI, incl. ArrayExpress), literature (PubMed / OpenAIRE), HuggingFace datasets, DataONE (eco / environmental), OmicsDI (proteomics / metabolomics), DANDI (neurophysiology), CZ CELLxGENE (single-cell), OpenML (ML datasets), RCSB PDB (structures), UniProtKB (proteins), the GWAS Catalog, GBIF (biodiversity), data.gov (US federal open data), and NASA CMR (Earth science) — deduplicated

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Maintainer setup documentation.

How to install the Data Aggregator MCP Server

{
  "mcpServers": {
    "data-aggregator": {
      "command": "uvx",
      "args": ["data-aggregator-mcp"],
      "env": {
        "NCBI_API_KEY": "your-value",
        "DATA_GOV_API_KEY": "your-value",
        "DEMO_KEY": "your-value",
        "DATAVERSE_BASE_URL": "your-value",
        "EMBEDDING_API_KEY": "your-value",
        "LLM_API_KEY": "your-value"
      }
    }
  }
}

Add to claude_desktop_config.json, then restart Claude Desktop.

Configuration

VariableDescriptionRequired
NCBI_API_KEYCredential the server authenticates with.Yes
DATA_GOV_API_KEYCredential the server authenticates with.Yes
DEMO_KEYCredential the server authenticates with.Yes
DATAVERSE_BASE_URLEndpoint or connection string the server talks to.Yes
EMBEDDING_API_KEYCredential the server authenticates with.Yes
LLM_API_KEYCredential the server authenticates with.Yes

Example prompts to try

  • “Use Data Aggregator to Prompts.”

Frequently asked questions

Find & fetch research datasets across Zenodo, DataCite, NCBI omics, and literature. Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.