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musharna

data-aggregator-mcp

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
NCBI_API_KEYNoRaises the NCBI E-utilities rate limit (3 → 10 req/s) used by the omics, literature, and taxonomy lookups.
UNPAYWALL_EMAILNoEnables the Unpaywall fallback leg of literature full-text retrieval.

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
searchA

Search public research-data archives, omics registries, and the literature for datasets, software, publications, and sequencing data. Fans out across Zenodo, DataCite (Dryad, Figshare, Dataverse, OSF, Mendeley), NCBI omics (GEO, SRA, BioProject), and literature (PubMed + OpenAIRE). Returns compact DataResource records; per-source failures are reported in errors{}. Use resolve for the full record (SRA resolve attaches the ENA FASTQ manifest; publication resolve attaches links[] to datasets/accessions, normalized identifiers (pmid/pmcid/doi), and — when open access — a full-text file), then fetch to download files. Pass organism= to expand the query with NCBI-Taxonomy synonyms; results carry normalized taxa[] + plant cross-links.

resolveA

Fetch the full DataResource for a known id (e.g. 'zenodo:7654321', 'datacite:10.5061/dryad.x', a bare Zenodo record id, or a DOI), including the complete files[] manifest. Publication resolve also attaches normalized identifiers (pmid/pmcid/doi) and, when open access, a full-text file. Pass cite= to render a citation onto the result (citation field); omitted means no citation.

fetchA

Download a resource's files to local disk and return the PATHS (never the file contents). Fetchable: Zenodo, SRA (ENA FASTQ), GEO supplementary files, and DataCite-discovered Figshare/Dataverse/OSF deposits (md5-verified), and open-access literature full text (EuropePMC XML / Unpaywall PDF, unverified); a DataCite Dryad id is manifest-only (resolve lists its files but fetch fails loud), and other DataCite repos plus paywalled/non-OA literature ids fail loud. Fails loud if selected files exceed max_bytes unless force=true. Verifies checksums; writes a .dataresource.json sidecar.

list_sourcesA

List wired data sources and their capabilities (layer, kinds, supported filters, auth requirement, rate limit, status).

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

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