ena-biosamples-mcp

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search_samples

Find ENA samples by species with optional country filter to retrieve sample records and total counts for genomics research.

Instructions

Find samples in the European Nucleotide Archive (ENA, EMBL-EBI) for a species.

Optionally filter by country of origin.

Returns the total number of matching samples plus up to limit records with accession, country, collection date, first public date, submitting centre and description.

Args: species: Scientific or common name, e.g. "Bos taurus" or "cattle". country: Country name, e.g. "United Kingdom" or "Kenya". Omit for all countries. limit: Max samples to return (1-100). Default 20. include_subspecies: Also include subspecies and breeds under this taxon.

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": {
      "species": "<species>"
    },
    "name": "search_samples"
  }
}

Input Schema

Name	Required	Description	Default
`limit`	No
`country`	No
`species`	Yes
`include_subspecies`	No

Output Schema

Name	Required	Description	Default
`query`	Yes
`taxon`	Yes
`samples`	Yes
`returned`	Yes
`country_filter`	Yes
`total_matching`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Sep 11, 2026

TDQS

A3.9/5.0

Behavior3/5

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

No annotations are provided, so the description carries the full burden. It does disclose the return shape (total count plus up to `limit` records with named fields) and the bounded limit range, which is useful. However, it says nothing about authentication, rate limits, error behavior, or how pagination beyond `limit` works.

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?

Front-loads the purpose, then the return summary, then the argument list in a clean labeled block. No sentence is redundant and the optional-filter caveat is placed where it matters.

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 an output schema present and all parameters fully documented, the description is nearly self-sufficient for correct invocation. The remaining gap is the absence of any sibling-routing or access/permission context, which matters given three adjacent tools.

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

Parameters5/5

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

Schema description coverage is 0%, so the description must compensate, and it does: every one of the four params is explained with meaning and examples (species as scientific or common name, country name with omit-for-all semantics, limit range 1-100 with default 20, include_subspecies covering subspecies and breeds).

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a concrete verb and resource ('Find samples in the European Nucleotide Archive for a species') and names the data source, which is more than a generic search label. It does not explicitly distinguish itself from siblings like get_biosample or count_records, so an agent must infer the boundary.

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

Usage Guidelines3/5

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

Usage is implied by the purpose and by the per-argument hints ('Omit for all countries', optional country filter). There is no explicit when-to-use/when-not guidance or mention of the alternatives (get_biosample, count_records), so the agent gets context but not routing rules.

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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