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Search MGnify Metagenomic Studies

ebi-metagenomics.studies.search
Read-onlyIdempotent

Search EBI's MGnify metagenomics archive for studies by free-text query (name/abstract/bioproject) and/or biome lineage (e.g. "root:Host-associated:Human"). Returns each study's accession, name, abstract, bioproject, sequencing centre, sample count, last-update date, and associated biome lineages. Data: EMBL-EBI MGnify (www.ebi.ac.uk/metagenomics), no auth required.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pageNoPage number, 1-indexed (default 1).
queryNoFree-text search across study name, abstract, and bioproject, e.g. "gut microbiome".
page_sizeNoNumber of studies to return per page, 1-25 (default 10).
biome_lineageNoFilter to studies classified under this biome lineage, e.g. "root:Host-associated:Human" or "root:Environmental:Aquatic:Marine". Get valid lineages from ebi-metagenomics.biome_browse.

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

A4.2/5.0
Behavior4/5

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

Annotations already cover read-only, idempotent, non-destructive behavior, so the description doesn't need to repeat that. It adds useful context: the data source (EMBL-EBI MGnify), that no auth is required, and the specific return fields. It does not mention pagination or default behavior, but the schema covers page/page_size limits, so this is acceptable.

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?

The description is three concise sentences: purpose and filtering, return fields, and data source/auth. It is front-loaded with the primary purpose and contains no filler or redundancy.

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 full schema coverage, the description is complete for a search tool. It explains how to filter, what is returned, and the data source. It could mention pagination behavior or what happens with no query, but those are inferable from the schema and common search semantics.

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 coverage is 100% with detailed descriptions for all four parameters. The description adds an example for biome_lineage and clarifies the free-text scope (name/abstract/bioproject), but these largely duplicate the schema descriptions. It doesn't add deeper semantics 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?

The description starts with a specific verb 'Search', identifies the resource 'EBI's MGnify metagenomics archive', and clarifies what is searched (free-text query and biome lineage). It also lists the returned fields, distinguishing it from sibling tools like ebi-metagenomics.studies.detail (which retrieves a single study) and ebi-metagenomics.biomes.browse (which lists biomes).

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?

The description clearly indicates this tool is for searching studies by free-text and/or biome lineage, and gives an example. It does not explicitly state when to use alternative tools (e.g., detail for a specific study), but the sibling names make that inferable. The schema also points to biome_browse for valid lineages, which is a helpful pointer.

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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