Data Aggregator MCP vs Zenodo

Data Aggregator MCP tools 6

• searchSearch 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, OpenNeuro), NCBI omics (GEO, SRA, BioProject), literature (PubMed + OpenAIRE), HuggingFace Hub (datasets), DataONE (eco/environmental federation), OmicsDI (proteomics/metabolomics), RCSB PDB (macromolecular structures), GWAS Catalog (genotype-phenotype studies), OpenML (ML datasets), DANDI (neurophysiology dandisets), and CZ CELLxGENE (single-cell datasets). 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=<name> to expand the query with NCBI-Taxonomy synonyms; results carry normalized taxa[] + plant cross-links. Pass disease=<name> to expand the query with MeSH descriptor synonyms (e.g. 'breast cancer' also matches 'Breast Neoplasms'); the expansion is echoed in mesh_expansion. Pass tissue=<name> to expand the query with UBERON synonyms (e.g. 'liver' also matches 'iecur'/'jecur'); the expansion is echoed in tissue_expansion. Pass chemical=<name> to expand the query with ChEBI compound synonyms (e.g. 'caffeine' also matches '1,3,7-trimethylxanthine'); the expansion is echoed in chemical_expansion. Pass assay=<name> to expand the query with EDAM assay/method synonyms (e.g. 'ChIP-seq' also matches 'ChIP-sequencing'); echoed in assay_expansion. Pass collapse_mirrors=true to opt into conservative cross-repo mirror collapse: same-dataset copies under different/no DOIs are folded into one record, with the folded copies annotated under mirrors[]. An ontology param that matches no term in its registry (e.g. organism='yeast' — NCBI Taxonomy indexes no such common name) is reported in unresolved[] and the search runs WITHOUT that expansion, so a dropped filter is never silent. Clients that support form elicitation are asked for a replacement term before the search runs.
• resolveFetch the full DataResource for a known id (e.g. 'zenodo:7654321', 'datacite:10.5061/dryad.x', 'hf:owner/name', 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=<format> to render a citation onto the result (citation field); omitted means no citation. Pass trust=true to attach retraction status (via Crossref) under trust{}. Pass fair=true to attach an RDA-grounded FAIRness score (0–100 + F/A/I/R sub-scores + actionable gaps) computed from the record under fair{}. Pass use=<intent> (commercial/redistribute/modify/ml-training) to attach a licence-compatibility advisory (ALLOW/REVIEW/DENY, not legal advice) under license_compat{}. Pass format=provenance for a one-call RO-Crate 1.1 data-availability dossier (under provenance{}) composing version-currency, licence+SPDX, FAIR score, retraction status, and the source/DOI/ID chain — it auto-attaches fair + trust.