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microbiomedata

nmdc-mcp

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get_samples_by_ecosystem

Retrieve biosamples filtered by ecosystem type, category, or subtype to study specific environments such as soil, marine, or host-associated microbiomes.

Instructions

Use this tool to find biosamples from specific ecosystem types, categories, or subtypes. Perfect for studying particular environments like soil, marine, or host-associated microbiomes.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
ecosystem_categoryNo
ecosystem_typeNo
ecosystem_subtypeNo
max_recordsNo
Behavior2/5

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

No annotations are provided, so the description must convey behavioral traits. It only implies a read-only operation ('find biosamples') but says nothing about authorization, rate limits, side effects, or return structure. This is insufficient for safe invocation.

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?

The description is two sentences with no superfluous text. It front-loads the core action and gives concrete examples. Could add parameter details without becoming verbose.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given four parameters, no annotations, no output schema, and many sibling tools, the description is too sparse. It lacks details on filtering behavior, valid values, output format, and pagination (max_records). The agent would likely need additional external knowledge to use this tool correctly.

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

Parameters2/5

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. It names three ecosystem-related parameters (category, type, subtype) and provides vague examples but does not explain valid values, format, or how they combine. The max_records parameter is omitted entirely.

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?

The description clearly states the tool retrieves biosamples by ecosystem type, category, or subtype, and provides examples (soil, marine, host-associated). It distinguishes from sibling tools that operate on other criteria like annotations or coordinates, but does not explicitly contrast.

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?

The description implies when to use the tool ('perfect for studying particular environments') but provides no guidance on when not to use it or how it compares to alternatives like get_samples_by_annotation or get_biosamples_for_study.

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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