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Glama

Metabolights

by io.github.pipeworx-io

Search Studies

search_studies
Read-onlyIdempotent

Search EBI MetaboLights, the metabolomics (metabolite / small-molecule) study repository, by keyword — disease, metabolite, organism, or analytical technique (e.g. "diabetes", "glucose NMR", "Homo sapiens LC-MS"). Returns matching study accessions (e.g. MTBLS1) with name and a short description.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax studies to return (default 15, max 100).
queryYesFree-text query, e.g. "type 2 diabetes urine NMR".

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "query": "type 2 diabetes urine NMR"
+  },
+  {
+    "limit": 25,
+    "query": "glucose LC-MS Homo sapiens"
+  }
+]
  2. First observed

TDQS

A4.4/5.0
Behavior4/5

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

Annotations already provide readOnlyHint, idempotentHint, etc. The description adds value by naming the specific repository (EBI MetaboLights) and clarifying the result includes accessions, name, and short description. No contradictions with annotations.

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?

Single paragraph front-loaded with action verb 'Search'. Every sentence provides key information: what it searches, how to search (examples), what it returns. No wasted words.

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?

No output schema, but description compensates by stating return format (accessions, name, short description). Parameter coverage perfect. Annotations handle safety/idempotency. Adequately complete for a search tool with two parameters.

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 covers 100% of parameters with descriptions. The description adds examples (e.g., 'diabetes', 'glucose NMR') and explains that query can include disease, metabolite, organism, or technique, enriching beyond schema's free-text description.

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 identifies the tool as searching the EBI MetaboLights repository by keyword, specifying resource type (metabolomics studies) and result format (accessions, name, description). It distinguishes from sibling 'get_study' by implying a list vs. single study retrieval.

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?

Provides explicit keyword examples and scope (disease, metabolite, organism, technique). While no direct 'when-not-to-use' is stated, the examples and reference to 'matching studies' imply search context, and sibling names like 'get_study' suggest alternatives for individual studies.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Metabolights toolsInspect
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TDQS

B3.3/5.0
Disambiguation1/5

The vast majority of tools (e.g., ask_pipeworx, ask_pipeworx_grounded, bet_research, polymarket_arbitrage, etc.) are unrelated to Metabolights and overlap heavily with each other in purpose. Only two tools (get_study and search_studies) are clearly distinct and relevant to the server's stated domain.

Naming Consistency2/5

Tool names are highly inconsistent, mixing snake_case (get_study, search_studies), camelCase (ask_pipeworx), and varied verb styles (e.g., validate_claim vs bet_research). No consistent pattern across the set.

Tool Count1/5

With 28 tools, the server is extremely overpopulated for its stated purpose (Metabolights). Only 2 tools actually pertain to metabolomics study access, while the remaining 26 are general-purpose or unrelated (e.g., bet_research, polymarket_edges), making the count highly inappropriate.

Completeness1/5

The Metabolights domain severely lacks completeness: only search_studies and get_study are provided, with no create, update, delete, or upload functionality. The server fails to cover essential operations for its supposed domain.

Resources