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biocontext-ai

nucleotide_archive_mcp

build_custom_query

Construct complex ENA queries by combining multiple field conditions with logical operators for precise filtering of nucleotide sequence data.

Instructions

Build a custom ENA query from field conditions.

Usage Tips

Advanced tool for constructing complex queries by combining multiple field conditions with logical operators. Use for precise filtering beyond what search_rna_studies() offers. Call get_available_fields() first to discover searchable field names.

Returns

dict Dictionary containing: - query: The constructed ENA query string - field_count: Number of conditions used - operator: Logical operator used - example_usage: How to use this query with other tools - error: Error message if any

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
field_conditionsYesList of conditions, each with "field", "operator" (=, >=, <=, !=, contains), and "value"
operatorNoLogical operator to combine conditions (AND or OR)AND

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

No annotations are provided, but the description details the return dictionary structure and indicates the tool constructs a query (non-destructive). It could be more explicit about side effects but is clear overall.

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?

Two concise sections (Usage Tips and Returns) plus a one-liner, no fluff, front-loaded with key info. Every sentence adds value.

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?

Given the output schema is described and sibling tools are complex, the description covers purpose, prerequisites, return structure, and use case. Minor gap: no mention of error handling details beyond the error field.

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 examples; the description adds the usage tip about get_available_fields, which indirectly helps with field_conditions, but doesn't elaborate further on parameter meanings 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 builds a custom ENA query from field conditions, distinguishing it from search_rna_studies by offering precise filtering.

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 provides when to use: 'for precise filtering beyond what search_rna_studies() offers', and suggests calling get_available_fields first, guiding the agent on prerequisites.

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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