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Bioportal Search

bioportal_search
Read-onlyIdempotent

Search ~1,300 biomedical ontologies for a term and get back the matching classes with their preferred label, synonyms, definition, ontology and permanent class IRI. AUTHORITATIVE for mapping free text to a coded clinical concept (NCIT, SNOMEDCT, LOINC, RXNORM, MESH, HPO, ICD10CM) — these are the curated terminologies themselves, not a description of them. Restrict with ontologies when you know which vocabulary you want.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax classes to return, 1-100 (default 25)
queryYesTerm to search for (e.g. "melanoma", "metformin")
_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.
ontologiesNoComma-separated ontology acronyms to restrict to (e.g. "NCIT,DOID,SNOMEDCT")
exact_matchNoOnly exact label/synonym matches (default false)
require_definitionsNoOnly return classes that carry a definition

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 the safety profile (readOnlyHint=true, destructiveHint=false, idempotentHint=true), so the burden on the description is reduced. The description adds valuable context beyond the annotations: the scope (~1,300 ontologies), the return structure (since no output schema exists), and the data-quality trait that results are the curated terminologies themselves rather than descriptive text. This is meaningful behavioral disclosure layered on top of the annotation hints.

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 sentences with zero filler. The core function is front-loaded, the authoritative usage note is bolded for salience, and the practical restriction tip closes it out. Every sentence earns its place — no redundant restatement of the tool name or schema content.

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?

Because there is no output schema, the description correctly takes on the burden of explaining the return value (classes with label, synonyms, definition, ontology, IRI), and it does so. Parameters are fully covered by the schema, and annotations carry the safety profile. The only minor gaps — pagination behavior and response limits — reside in the schema's `limit` parameter, so the tool is adequately specified for an agent to call correctly.

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 all six parameters (limit, query, _apiKey, ontologies, exact_match, require_definitions) are already documented in the schema. The description's mention of restricting with `ontologies` adds a small usage hint beyond the schema, but it largely restates the parameter's purpose. Baseline 3 is appropriate since the schema carries the parameter documentation burden.

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 opens with a specific verb-resource pair ('Search ~1,300 biomedical ontologies for a term') and enumerates exactly what is returned (preferred label, synonyms, definition, ontology, permanent class IRI). This clearly separates it from sibling tools: bioportal_class (retrieving a specific class), bioportal_mappings, and bioportal_ontologies (listing ontologies).

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 capitalized 'AUTHORITATIVE for mapping free text to a coded clinical concept' establishes a clear when-to-use signal, and the closing tip 'Restrict with `ontologies` when you know which vocabulary you want' gives actionable selection guidance. The phrase 'not a description of them' implies an exclusion boundary against ontology-level tools, though it never explicitly names the alternative sibling or states a when-not-to-use case.

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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