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Browse MGnify Biome Classification Tree

ebi-metagenomics.biomes.browse
Read-onlyIdempotent

Browse MGnify's environment classification tree starting at a given lineage — returns the queried biome plus every descendant beneath it (not just immediate children), e.g. lineage "root" for the entire tree or "root:Host-associated" for just that subtree. Returns each biome's lineage, name, and sample count — use the returned lineage as the biome_lineage filter in ebi-metagenomics.study_search. Data: EMBL-EBI MGnify (www.ebi.ac.uk/metagenomics), no auth required.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pageNoPage number, 1-indexed (default 1).
lineageNoBiome lineage to browse the descendant subtree of, e.g. "root" (entire tree), "root:Host-associated", or "root:Environmental:Aquatic:Marine". Defaults to "root". Returns the queried biome plus every descendant beneath it, not just immediate children.
page_sizeNoNumber of biomes to return per page, 1-50 (default 20).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint as false. The description adds valuable behavioral context: it returns the queried biome plus every descendant (not just immediate children), includes lineage, name, and sample count per biome, and notes that no authentication is required. These details are not present in annotations, enriching the agent's understanding.

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 well-structured with a clear opening, examples, and a usage note. It is slightly long but every sentence contributes meaningful information without redundancy. It front-loads the core behavior and then adds practical guidance.

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?

For a tool with an output schema (which presumably details the return structure), the description goes beyond by stating exactly what fields are returned (lineage, name, sample count) and its intended downstream use. It covers the key aspects an agent needs to call it correctly, including lineage format and data source, without being excessive.

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?

The input schema provides detailed descriptions for all three parameters (page, lineage, page_size) with examples and ranges, covering 100% of parameters. The description's mention of lineage examples ('root', 'root:Host-associated') overlaps with schema content, adding minimal extra value. This aligns with the baseline score of 3 for high schema coverage.

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?

The description clearly states the action (browse), the resource (MGnify's environment classification tree), and the specific behavior (returns queried biome plus all descendants). It provides concrete examples for the lineage parameter, distinguishing it from any ambiguous tree-browsing tool.

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?

It explicitly explains when to use this tool by stating 'use the returned lineage as the biome_lineage filter in ebi-metagenomics.study_search' and gives examples of valid lineages. It does not explicitly mention alternatives, but its purpose is narrowly defined, and the downstream usage 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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