nucleotide_archive_mcp

get_study_details

Retrieve comprehensive metadata for an ENA study, including abstract, publications, and institution details, to verify relevance before downloading.

Instructions

Get comprehensive metadata for a specific ENA study including publications.

Usage Tips

Call after search_rna_studies() to verify a study matches your research needs before downloading. Returns detailed study description, publication links, and institutional metadata. Use this to check publications array for PubMed IDs.

Returns

dict Dictionary containing: - accession: Study accession - title: Brief study title - description: Detailed study description (full abstract/methods) - publications: List of publications with pubmed_id and source - center_name: Submitting institution - alias: Submitter's study name (often GSE accession for GEO) - data_type: Usually "STUDY" - status: "public" or "private" - first_public: Date made public (YYYY-MM-DD) - last_updated: Last modification date (YYYY-MM-DD) - file_report_links: Direct API links for file reports - error: Error message if study not found or if request fails

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "study_accession": "<study_accession>"
    },
    "name": "get_study_details"
  }
}

Input Schema

Name	Required	Description	Default
`study_accession`	Yes	Study accession from search results. Accepts SRP/ERP/DRP or PRJNA/PRJEB/PRJDB formats

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.0.7Jun 21, 2026

TDQS

A4.1/5.0

Behavior3/5

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

With no annotations, the description details the return structure but does not disclose any side effects, authentication needs, or rate limits. However, for a read-only 'get' operation, the transparency is adequate.

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

Conciseness5/5

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

Well-structured with clear sections: description, usage tips, returns. Every sentence adds value, and it is front-loaded with the purpose.

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 single parameter, no annotations, and detailed return description, the tool definition is complete for its purpose. The description covers all necessary aspects.

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

Parameters3/5

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

Input schema has 100% description coverage for the single parameter 'study_accession'. The description adds no additional semantics beyond the schema's description and examples.

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 it 'Get comprehensive metadata for a specific ENA study including publications.' It specifies the verb, resource, and scope, distinguishing it from siblings like 'get_study_publications' which only returns publications.

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?

Provides explicit usage tip: 'Call after search_rna_studies() to verify a study matches your research needs before downloading.' It also mentions checking publications array for PubMed IDs, giving clear context for when to use.

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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