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biocontext-ai

nucleotide_archive_mcp

get_study_publications

Retrieve comprehensive publication details for RNA study accessions, including author ORCIDs, affiliations, citation counts, and full-text links from ENA and Europe PMC.

Instructions

Get detailed publication information for a study from ENA and Europe PMC.

Usage Tips

Call after search_rna_studies() to get full publication metadata including author ORCID IDs, affiliations, citation counts, and full-text links. Enriches basic publication info from get_study_details() with complete bibliographic data from Europe PMC.

Returns

dict Dictionary containing: - accession: Study accession - publication_count: Number of publications found - publications: List of detailed publication objects, each with: - pubmed_id: PubMed ID - pmcid: PubMed Central ID (if available) - doi: Digital Object Identifier (if available) - title: Publication title - authors: List of author names - first_author: First author name - last_author: Last author name - author_details: Detailed author info with ORCID and affiliations - journal: Journal name - journal_issn: Journal ISSN - publication_year: Year published - publication_date: Full publication date - abstract: Publication abstract - citation_count: Times cited - is_open_access: Whether open access - in_epmc: Whether in Europe PMC - in_pmc: Whether in PubMed Central - has_pdf: Whether PDF available - full_text_urls: Available full text links - error: Error message if any

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
study_accessionYesStudy accession from search results. Accepts SRP/ERP/DRP or PRJNA/PRJEB/PRJDB formats

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

With no annotations, the description provides a detailed return structure covering all fields including author details, citation counts, and open access status. It implies read-only behavior by stating it 'gets' data from external sources. No destructive effects are mentioned, which is appropriate.

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 well-structured with a brief introductory sentence, a 'Usage Tips' section, and a detailed 'Returns' section. While fairly long, the detailed output documentation is necessary given no separate output schema. The information is front-loaded and each part serves a purpose.

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

Completeness4/5

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

The description covers the input parameter, usage context (after search_rna_studies), and a comprehensive return structure. It lacks explicit error handling details (though 'error' field is mentioned). Overall, it is quite complete for a tool with one parameter and no annotations.

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?

The single parameter 'study_accession' is well-documented in the input schema with description and examples. The tool description does not add additional semantics beyond what the schema already provides. Schema coverage is 100%, so baseline is 3.

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 verb 'Get', the resource 'detailed publication information for a study', and the sources 'ENA and Europe PMC'. It differentiates from siblings like get_study_details by saying it enriches basic info with complete bibliographic data.

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?

Explicitly says to call after search_rna_studies() and that it enriches get_study_details(). This provides clear context for when to use the tool versus alternatives, though it does not state when not to use it.

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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