Data Aggregator MCP Server

One MCP server to find and fetch research data across archives, omics registries, and literature - behind a single normalized model. Its 26 documented tools cluster into read & search, shared, data, organism. It runs locally over stdio via the published package.

People who work with bioinformatics, datacite and datasets and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-09-17 · ★ 3 · #36 OF 71 MAINTAINED SCIENCE & HEALTH · VERIFIED 2026-09-18

MIT · Python servers · how we verify → /methodology

01 · Install Data Aggregator

before you install - you'll need

Set DATA_AGGREGATOR_MCP_LIVE before connecting. NCBI_API_KEY is optional or environment-specific per the README.

Claude Code

claude mcp add musharna-data-aggregator-mcp -- uvx data-aggregator-mcp

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "musharna-data-aggregator-mcp": {
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license MIT - declared in the repository

pypi package data-aggregator-mcp - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.musharna is GitHub-verified and matches the repo owner

03 · What Data Aggregator can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can find datasets for a topic, optionally scoped to an organism, and find the datasets / accessions behind a paper.

Capability map

Tools grouped from the project's README - what Data Aggregator lets an agent do.

read & search

2 tools - e.g. Zenodo, SRA, GEO, DataONE (Member-Node objects,; walk the end-to-end search → resolve → fetch flow.

Fetchable · search_resolve_fetch

Shared

2 tools - e.g. same BioProject/SRA/GEO accession on ≥2 records → joinable key.; same doi/pmid/pmcid across records → same work / paper↔data link.

shared_accession · shared_identifier

Data

2 tools - e.g. find datasets for a topic, optionally scoped to an organism.; find the datasets / accessions behind a paper.

find_data · data_behind_paper

Organism

1 tool - e.g. expand the query with NCBI-Taxonomy synonyms; the expansion is

organism

Sources

1 tool - e.g. restrict the fan-out, e.g. ["omics"].

sources

Size

1 tool - e.g. max results (1–50).

size

Kind

1 tool - e.g. keep only dataset / sequencing_run / study / publication /

kind

Rank

1 tool - e.g. relevance (default) or semantic (re-rank the fetched page by

rank

Latest releases

v0.45.3 · 2026-07-28

v0.45.3 · Security fix, and a correction to v0.45.2. Take this instead of 0.45.2 if you · run the HTTP transport, or if you call operate/fetch on records you did not · publish yourself. · Fixed · A redirect bypassed…

v0.45.2 · 2026-07-28

v0.45.2 · Security fix. Upgrade from 0.45.1 if you run the HTTP transport, or if you call · operate/fetch on records you did not publish yourself. · Fixed · A record's file URL could make the server read addresses the…

v0.45.1 · 2026-07-28

v0.45.1 · Security fix. Upgrade from 0.45.0 if you rely on licence verdicts. · Fixed · A hostile licence URL could mint a permissive verdict. host_matches already · rejected a domain sitting in someone else's path, but…

04 · Who maintains Data Aggregator

Data Aggregator is maintained by musharna. We track 8 MCP servers from musharna - 8 actively maintained, 14 combined GitHub stars, oldest repo from May 2026. Full record: all servers from musharna.

05 · Facts

repository: github.com/musharna/data-aggregator-mcp
category: science & health - ranked #36 of 71 actively-maintained science & health servers as of 2026-09-18.
release cadence: 9 releases in the last 90 days (latest 2026-07-28)
registry: io.github.musharna/data-aggregator-mcp (active, first published 2026-05-30 · 35 versions)
packages: pypi:data-aggregator-mcp

06 · Data Aggregator FAQ

Is Data Aggregator still maintained?

Yes - as of 2026-09-18, its last commit was 2026-09-17 and it shipped 9 releases in the last 90 days. We re-verify nightly.

What can Data Aggregator do?

With this server connected, an agent can find datasets for a topic, optionally scoped to an organism, and find the datasets / accessions behind a paper.

How do I install Data Aggregator?

Run `uvx data-aggregator-mcp`. The README documents 2 environment variables (NCBI_API_KEY, DATA_AGGREGATOR_MCP_LIVE) to set first. Set DATA_AGGREGATOR_MCP_LIVE before connecting. NCBI_API_KEY is optional or environment-specific per the README. You can also paste the ready-made client config above.

Does Data Aggregator run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Data Aggregator

Alternatives to Data Aggregator

Maintained science & health servers if Data Aggregator isn't the fit.

More science & health MCP servers · Pubcrawl · Redacta MCP · DICOM/HL7/FHIR Interoperability MCP Server · Omophub MCP · Kaiord

More Python MCP servers · Jobd · Ldraw MCP · Plant Genomics · Openshorts · Agent SUMO · see all