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Mgnify Biomes

mgnify_biomes
Read-onlyIdempotent

List MGnify's controlled biome vocabulary — the ~492 colon-delimited lineages (root:Host-associated:Human:Digestive system:Large intestine:Fecal, root:Environmental:Aquatic:Marine…) that every MGnify study is classified under. This is the lookup step before filtering studies or genomes by environment: the lineage strings are exact and are not guessable. Optionally narrow to one subtree by prefix.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum lineages to return, 1-200 (default 20).
lineage_prefixNoKeep only lineages starting with this, e.g. "root:Host-associated:Human" or "root:Environmental".

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already cover readOnly/idempotent/openWorld safety, so the description's job is to add domain context — and it does: vocabulary size (~492), delimiter format, root prefixes, and the non-guessable exactness of strings. It stops short of describing pagination or full return shape.

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?

Three tight sentences, front-loaded with the resource, then the why, then the optional narrowing. Zero filler.

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

Completeness5/5

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

No output schema exists, and the description adequately conveys what comes back (lineage strings in a controlled vocabulary) plus the optional prefix narrowing. Nothing essential to correct invocation is missing.

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 description coverage is 100%, so both parameters are already documented in the schema; the description only echoes 'narrow to one subtree by prefix'. Baseline 3 applies since the description adds no syntax or format detail 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?

Specific verb+resource: 'List MGnify's controlled biome vocabulary', with concrete examples of the colon-delimited lineages it returns. It is immediately distinguishable from siblings like mgnify_search_studies or mgnify_genomes, which filter using this vocabulary rather than return it.

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?

Explicitly positions itself as 'the lookup step before filtering studies or genomes by environment' and explains why it is needed ('lineage strings are exact and are not guessable'). It does not name the specific sibling tools to call next, but the usage context is clear.

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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