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musharna

data-aggregator-mcp

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Search public research data archives, omics registries, and literature for datasets, software, publications, and sequencing data across Zenodo, DataCite, NCBI omics, and PubMed/OpenAIRE.

Instructions

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesFree-text search query
sizeNoMax results (1-50, default 10)
sourcesNoRestrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature
organismNoOptional organism name. Resolved via NCBI Taxonomy; the query is expanded with the canonical name + synonyms (e.g. 'Orobanche aegyptiaca' also matches 'Phelipanche aegyptiaca'). The expansion is echoed in taxon_expansion.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
totalYes
countYes
resultsNo
errorsNo
next_cursorNo
taxon_expansionNo
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description bears full responsibility for behavioral disclosure. It details the fan-out across sources, returns compact records, reports per-source failures in errors{}, and explains taxon expansion. While it does not explicitly confirm read-only behavior or mention rate limits, the description is sufficiently transparent for a search tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single paragraph that efficiently conveys the tool's purpose, sources, usage flow with siblings, and parameter nuances. While it could be structured with bullet points for easier scanning, it is concise and front-loads the main action, earning each sentence.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (multiple sources, related tools, and output schema), the description is thoroughly complete. It covers the search action, return type (compact DataResource records), error reporting, relation to resolve and fetch, and the organism parameter's behavior. The existence of an output schema reduces the need to explain return values in detail, and the description leverages this well.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, providing a baseline of 3. The description adds value by explaining the free-text nature of query, the range and default for size, listing available sources, and detailing the organism parameter's NCBI Taxonomy expansion and the resulting taxon_expansion field. This goes beyond the schema's basic descriptions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool searches public research-data archives, omics registries, and literature, listing specific sources. It distinguishes itself from siblings by explicitly directing to 'use resolve for the full record... then fetch to download files,' making its role as the search entry point unambiguous.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear guidance on when to use this tool (searching) and when to use siblings (resolve for full records, fetch for downloads). It also explains the organism parameter for query expansion. However, it does not explicitly state when not to use this tool, which would strengthen the guidelines.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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