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biocontext-ai

nucleotide_archive_mcp

find_studies_by_publication

Search for European Nucleotide Archive studies using a PubMed ID. Due to API limitations, this tool reports an error and recommends using keyword search and study details to find matching publications.

Instructions

Find ENA studies by PubMed ID (API limitation - returns error with workaround).

Usage Tips

ENA Portal API doesn't expose pubmed_id as a searchable field. This tool documents the limitation for LLM awareness. Instead: use search_studies_by_keywords() with publication terms, then call get_study_details() to check the publications array for matching PubMed IDs.

Returns

dict Dictionary containing: - error: API limitation message with recommended workflow - pubmed_id: Provided PubMed ID - count: Always 0 - studies: Always empty list

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pubmed_idYesPubMed ID to search for. Note: This tool has known API limitations and will return an error with alternative instructions

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

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

With no annotations, the description fully discloses the tool's behavior: it returns an error message with recommended workflow, count always 0, studies empty. No hidden surprises.

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?

Well-structured with headers and bullet points, but could be slightly more concise. Every sentence adds value, but the returns section is somewhat redundant with schema.

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?

For a simple tool with one parameter and an output schema, the description fully covers what to expect, including error handling and alternative workflow. No gaps.

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?

Schema coverage is 100% with description and examples for the single parameter. Description adds context about API limitation but does not significantly augment the parameter's meaning beyond the schema.

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 finds ENA studies by PubMed ID, then immediately notes the API limitation and provides an alternative workflow. It distinguishes itself from sibling tools like search_studies_by_keywords.

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

Usage Guidelines5/5

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

Explicitly tells when not to use this tool and provides an alternative: use search_studies_by_keywords() with publication terms, then get_study_details(). This is perfect guidance.

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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