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Bioportal Ontologies

bioportal_ontologies
Read-onlyIdempotent

List the biomedical ontologies BioPortal carries — acronym, full name and type — so you can pick the right vocabulary acronym before searching or looking up a class. AUTHORITATIVE catalogue of what is available in BioPortal. Pass filter to narrow by acronym or name substring.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax ontologies to return, 1-200 (default 50)
filterNoCase-insensitive substring of the acronym or name (e.g. "snomed", "cancer")
_apiKeyNoYour own BioPortal API key (free, https://bioportal.bioontology.org/accounts/new). Optional — without one the call uses a shared key that NCBO rate-limits across all of its users.

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 establish readOnlyHint, idempotentHint, openWorldHint, and non-destructive behavior. The description adds the 'AUTHORITATIVE catalogue' claim, the returned fields, and the pre-search workflow context, which goes beyond annotations. It does not mention rate limits or pagination, but those are covered in the input schema, and the annotation coverage lowers the burden.

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 short sentences with the main action and purpose front-loaded. The AUTHORITATIVE catalogue note and the filter guidance each earn their place; there is no redundancy or 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?

For a zero-required-parameter read-only listing tool with full schema coverage, the description plus schema fully cover how and when to call it correctly. The description even enumerates the output fields (acronym, full name, type), compensating for the lack of an output schema.

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 the baseline is 3. The description adds workflow meaning to `filter` by framing it as narrowing the catalogue, but it provides no additional semantic detail beyond what the schema already documents for `limit` and `_apiKey`.

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?

States a specific verb ('List'), a clear resource ('biomedical ontologies BioPortal carries'), and the output content ('acronym, full name and type'). It also frames the workflow purpose ('so you can pick the right vocabulary acronym before searching or looking up a class'), distinguishing it from siblings like bioportal_search, bioportal_class, and bioportal_mappings.

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 clear context: use this tool to choose a vocabulary acronym before performing a search or class lookup, and pass `filter` to narrow by acronym or name. It does not explicitly name sibling alternatives or state when not to use them, so it misses the highest bar, but the intended usage is well implied.

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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