musharna/data-aggregator-mcp

Search 20 research-data sources at once (data archives, omics repositories and
papers) and get one list back. Organism, disease and tissue names are expanded
with their synonyms in the 12 sources that accept them, records that share a DOI are collapsed to one, and downloads
are checked against the source's checksum where it publishes one.
mcp-name: io.github.musharna/data-aggregator-mcp
Install
Claude Code:
VS Code and Cursor: the buttons above. Any other MCP client: run
uvx data-aggregator-mcp as a stdio server.
Claude Desktop, pip, and the operate extra
Claude Desktop (claude_desktop_config.json) and most other clients:
With pip:
operate (SQL and previews over remote files) needs an optional extra:
pip install "data-aggregator-mcp[operate]".
What you can ask
**"Find transcriptomes for Orobanche aegyptiaca."** The species has been renamed.
NCBI Taxonomy maps it to *Phelipanche aegyptiaca*, and the sources that accept
synonyms match both names (the demo above).
**"What data came out of this paper?"**
**"Can I train a model on this dataset?"**
The verdict is read from the record's licence metadata. It is advice, not a legal
opinion.
resolve also renders citations in any CSL style, checks Crossref for
retractions, scores FAIRness, and exports Croissant or RO-Crate. relate reports
how a set of records connect (a shared accession, DOI or explicit link).
How a search runs
A source that fails is named in the result's errors, never dropped silently.
Compared with other servers
| Server | Searches | One search | Checksum | Remote SQL | Licence check |
| --- | --- | :---: | :---: | :---: | :---: |
| **data-aggregator-mcp** | 20 sources: data archives, omics, papers | yes, DOI dedup | where published | yes | yes |
| Mobus | 20 general and ML data platforms | yes | — | row preview | yes |
| paper-search-mcp | papers: arXiv, PubMed, OpenAlex, Crossref and more | yes, deduplicated | — | — | — |
| ToolUniverse | 1000+ tools: models, datasets, APIs, packages | papers | — | — | — |
| BioMCP | genes, variants, trials, drugs, proteins, papers | yes (search all) | — | — | — |
— means the project's README doesn't describe it (READMEs read 2026-10-04).
Where they are ahead: BioMCP reaches clinical trials, ChEMBL and AlphaFold, which
this server doesn't; ToolUniverse covers far more ground overall; paper-search-mcp
covers far more literature sources; Mobus also compares datasets and checks schema
compatibility. More detail: docs/POSITIONING.md.
Sources
| Source | Discover | Fetch | Checksum |
| ---------------------------- | :------: | :---------------: | :--------------: |
| Zenodo | ✅ | ✅ | md5 |
| DataCite → Figshare | ✅ | ✅ | md5 |
| DataCite → Dataverse | ✅ | ✅ | md5 |
| DataCite → OSF | ✅ | ✅ | md5 |
| DataCite → Dryad | ✅ | manifest only¹ | sha-256 (listed) |
| DataCite → Mendeley & others | ✅ | — | — |
| NCBI SRA | ✅ | ✅ (ENA FASTQ) | md5 |
| NCBI GEO | ✅ | ✅ (suppl/) | none² |
| NCBI BioProject | ✅ | → SRA links | — |
| PubMed / OpenAIRE | ✅ | ✅ (OA full text) | none³ |
| Hugging Face datasets | ✅ | ✅ (resolve URL) | none² |