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ncbo

bioportal-mcp

by ncbo

search_ontology_terms

Search across BioPortal ontologies to find ontology terms by query. Retrieve term IDs, labels, ontologies, and URLs.

Instructions

Search for ontology terms in BioPortal.

This function searches across BioPortal ontologies for terms matching the given query. It returns a list of tuples containing the term ID, preferred label, ontology, and ontology URL.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesThe search term (e.g., "melanoma", "breast cancer", "neuron").
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).
require_exact_matchNoIf True, only return exact matches (default: False).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries full burden. It does not disclose any behavioral traits like case sensitivity, pagination, performance implications, or side effects. The schema provides some details but the description adds little beyond the basic search operation.

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?

The description is two sentences, concise, and front-loaded with the purpose. Every sentence adds value without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the absence of annotations and the presence of an output schema, the description should provide more contextual completeness about usage and behavior. It lacks guidelines and behavioral details, making it insufficient for full understanding.

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 baseline is 3. The description does not add any additional meaning beyond the schema; it only mentions the return format. No extra parameter context.

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 states the tool searches for ontology terms in BioPortal and specifies the return format (list of tuples with term ID, label, ontology, URL). It distinguishes from siblings like get_ontology_analytics and search_ontology_properties by focusing on 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 Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives, no exclusions, and no context about prerequisites or limitations. It only describes the basic function.

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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