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mesa-clm

mesa-clm

by idss-mesa
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Python
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mesa_ols_list_ontologies

Retrieve paginated lists of ontologies from EMBL-EBI OLS4 to discover available biological and chemical vocabularies like ENVO, GO, and CHEBI.

Instructions

List ontologies available in the EMBL-EBI Ontology Lookup Service (OLS4), paginated. Returns 266+ ontologies (ENVO, GO, CHEBI, etc.).

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "mesa_ols_list_ontologies"
  }
}

Input Schema

NameRequiredDescriptionDefault
pageNoZero-indexed page number.
sizeNoResults per page (1–200).

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.6/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral burden. It does disclose two useful traits — results are paginated and the corpus is 266+ ontologies — but says nothing about rate limits, authentication, or the shape of each returned ontology record.

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?

Two tight sentences, front-loaded with the action and service, followed by the payoff (count and example ontologies like ENVO, GO, CHEBI) that helps an agent confirm it found the right catalog. No filler.

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 simple read-only, zero-required-parameter list tool with fully documented params and no output schema, the description is nearly sufficient. The one gap is that it never hints at what an ontology entry contains (id, title, prefix), which would help the agent use the result.

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%, with both page and size fully documented in the schema including defaults and bounds (1–200). The description adds only the word "paginated," which the schema already conveys, so the baseline 3 is correct.

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?

States a specific verb and resource ("List ontologies") plus the backing service (EMBL-EBI OLS4), which cleanly separates it from the singular sibling mesa_ols_get_ontology. It stops short of explicitly naming that sibling or any other alternative, so differentiation is implied by wording rather than stated.

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?

Usage is only implied: an agent can infer this is the entry point for discovering which ontologies exist before drilling into terms or a single ontology. There is no explicit when-to-use, when-not-to-use, or pointer to mesa_ols_get_ontology / mesa_ols_search_terms as follow-ups.

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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