ena-biosamples-mcp

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get_biosample

Fetch a complete EMBL-EBI BioSamples record by accession to inspect organism, tissue, breed, sex, and geographic location metadata.

Instructions

Get an EMBL-EBI BioSamples record with all its attributes.

Attributes include organism, geographic location, tissue, breed and sex where submitted.

Args: accession: BioSamples accession, e.g. "SAMEA7658521". Use the accession returned by search_samples.

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": {
      "accession": "<accession>"
    },
    "name": "get_biosample"
  }
}

Input Schema

Name	Required	Description	Default
`accession`	Yes

Output Schema

Name	Required	Description	Default
`name`	No
`tax_id`	No
`accession`	Yes
`update_date`	No
`release_date`	No
`characteristics`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Sep 11, 2026

TDQS

A4.1/5.0

Behavior3/5

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

No annotations are provided, so the description carries the disclosure burden. It usefully signals that the full record's attributes are returned and that some fields exist only 'where submitted' (i.e. may be absent), which sets expectations. However, it says nothing about permissions, rate limits, or failure behavior when an accession is invalid.

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 with the core action, and the attribute list is a single efficient clause. The 'Args:' block is slightly formal/verbose for a one-parameter tool but still earns its place by clarifying the accession format.

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?

An output schema exists, so return-value documentation is not required, and the single parameter is fully explained. What remains thin is operational context (auth, error handling), but for a simple one-param read tool the description is largely 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 description coverage is 0%, so the description must compensate, and it does: it defines 'accession' as a BioSamples accession, gives a concrete example format ('SAMEA7658521'), and specifies the authoritative source (the output of search_samples). Only minor detail like locale/validation rules is missing.

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 ('Get an EMBL-EBI BioSamples record') and enumerates the content it returns (organism, geographic location, tissue, breed, sex). It also routes the agent away from the sibling search_samples by tying the accession to that tool's output, so it is distinguishable without opening either schema.

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?

'Use the accession returned by search_samples' gives a clear usage path and identifies the correct upstream tool. It stops short of stating when NOT to use this tool or what to do if no accession is known, so it is strong but not exhaustive.

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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