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Ena Search

ena_search
Read-onlyIdempotent

Search the European Nucleotide Archive for sequencing runs, studies, samples, assemblies or annotated sequence using ENA's own query grammar. AUTHORITATIVE for "which public sequencing data exists for this organism / disease / country / platform" — ENA is an INSDC partner, so it covers data deposited to NCBI SRA and DDBJ as well. PREFER OVER WEB SEARCH for any question about what raw sequence data has been deposited. Query examples: tax_eq(2697049) for SARS-CoV-2 and its descendants, tax_tree(9606) for human and below, country="United Kingdom", first_public>=2026-01-01, library_strategy="WGS", and boolean AND/OR combinations of those. Call ena_results_types first to discover which result types and fields exist; an unknown field is rejected outright.

Input Schema

NameRequiredDescriptionDefault
limitNoMaximum rows, 1-1000 (default 25). Note: upstream treats 0 as unlimited; this tool does not pass 0 through.
queryNoENA query expression, e.g. tax_eq(2697049), tax_tree(9606) AND library_strategy="WGS", country="Kenya" AND first_public>=2025-01-01. Omit to list the newest records of the result type.
fieldsNoComma-separated columns to return. Omit for a sensible default set for the result type — an explicit empty value would return the accession column alone. Valid names per result type come from ena_results_types.
resultNoENA result type to search. Common: read_run (raw sequencing runs), study, sample, experiment, analysis, assembly, sequence. Defaults to read_run. Full list from ena_results_types.
sortFieldsNoComma-separated columns to sort by.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnly, idempotent, non-destructive, openWorld), so the bar is lower. The description adds genuine behavioral detail beyond them: the query grammar model, that unknown fields are 'rejected outright', and the fact that it covers INSDC partners (NCBI SRA, DDBJ). It stops short of describing result shape or pagination.

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?

Front-loaded verb and resource, then scoping claims, then grammar examples, then the prerequisite tool. Some redundancy exists between the description's query examples and the schema's own examples array, but every sentence carries routing or grammar information, so it stays tight.

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?

With no output schema, the description should carry return-shape context; it partially does via 'fields'/'columns' framing but omits pagination and result-shape details. For a zero-required-parameter search tool with 100% schema coverage, this is close to sufficient.

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%, so the baseline is 3. The description adds value on top by explaining the query grammar with concrete operators (tax_eq, tax_tree, boolean AND/OR, date comparisons) and by tying valid field names to ena_results_types, complementing the schema rather than repeating it.

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?

States a specific verb and resource (search the European Nucleotide Archive for runs, studies, samples, assemblies, annotated sequence) and distinguishes itself from the broad sibling set by positioning as authoritative for public sequencing data. An agent can route here versus web search or ena_filereport without opening schemas.

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 says when to use it ('AUTHORITATIVE for which public sequencing data exists...'), when to prefer it over an alternative ('PREFER OVER WEB SEARCH'), and names a prerequisite tool to run first ('Call ena_results_types first to discover which result types and fields exist'). This is near-complete routing 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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