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ncbo

bioportal-mcp

by ncbo

search_ontology_properties

Search for ontology properties across BioPortal by label or ID. Filter by ontology, property type, exact match, or definition status.

Instructions

Search for ontology properties in BioPortal.

This function searches for ontology properties (object properties, annotation properties, datatype properties) by their labels and IDs across BioPortal ontologies.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesThe search term (e.g., "has part", "related to", "has dimension").
api_keyNoBioPortal API key. If not provided, uses BIOPORTAL_API_KEY environment variable.
ontologiesNoComma-separated list of ontology acronyms to search in (e.g., "NCIT,GO,HP"). If None, searches across all ontologies.
max_resultsNoMaximum number of results to return (default: 10).
property_typesNoComma-separated list of property types to filter by: "object", "annotation", "datatype". If None, returns all property types.
require_definitionsNoIf True, only return properties that have definitions (default: False).
require_exact_matchNoIf True, only return exact matches by property id, label, or generated label (default: False).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations provided, so description bears full burden. It states it searches by labels and IDs but lacks details on idempotency, side effects, or expected response specifics. Output schema exists, reducing need to explain return values, but behavioral traits like rate limits or necessary permissions are omitted.

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 sentences, no redundant information, clear and direct.

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?

Given the tool's complexity (7 parameters, output schema), the description covers the core purpose and adds context on property types and scope. Could mention relationship to sibling tool for differentiation, but overall adequate.

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 coverage 100% with detailed parameter descriptions. Description adds value by specifying that search is by labels and IDs, which is not in schema. This clarifies the search mechanism.

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?

Description clearly states it searches for ontology properties, lists types (object, annotation, datatype), and mentions operation across BioPortal ontologies. Distinguishes from sibling tools which are analytics and term search.

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?

Description gives context but does not provide explicit guidance on when to use this tool over siblings, nor does it mention conditions where it should not be used.

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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