data-aggregator-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| NCBI_API_KEY | No | Raises the NCBI E-utilities rate limit (3 → 10 req/s) used by the omics, literature, and taxonomy lookups. | |
| UNPAYWALL_EMAIL | No | Enables the Unpaywall fallback leg of literature full-text retrieval. |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| 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
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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