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musen-lab

CEDAR MCP Server

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by musen-lab

get_ontology_class_tree

Retrieve the hierarchical tree structure for an ontology class, showing its ancestor path and sibling nodes to understand its position in the ontology hierarchy.

Instructions

Fetch the hierarchical tree structure for a given class in an ontology.

Use this tool to retrieve the ancestor path and sibling nodes for a specific class IRI in a BioPortal ontology. This is useful for understanding where a term sits in the ontology hierarchy.

Args: class_iri: IRI of the class to get the tree for (e.g., "http://purl.obolibrary.org/obo/MONDO_0005180") ontology_acronym: Ontology acronym to search within (e.g., "MONDO", "CHEBI")

Returns: BioPortal response containing the class tree hierarchy

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
class_iriYes
ontology_acronymYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

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 burden. It clearly states the tool fetches a tree structure and describes the return. However, it does not disclose error behavior, authentication requirements, or explicitly confirm read-only safety, though the verb 'Fetch' implies non-mutating.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with a summary, usage guidance, and Args/Returns sections. It is not overly verbose, though the first two sentences are slightly redundant.

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?

The description is complete for a simple read-only tool: it explains what it does, when to use it, both parameters with examples, and the return value. Given the output schema exists, it does not need to detail response structures further.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema properties have no descriptions (0% coverage), so the description must compensate. It provides explicit explanations with examples for both class_iri and ontology_acronym, fully making up for the schema gap.

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 uses the specific verb 'Fetch' with resource 'hierarchical tree structure' and clearly defines scope as a specific class IRI in a BioPortal ontology. It distinguishes from sibling tools like get_branch_children by specifying that it returns ancestor path and sibling nodes.

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 description explicitly states 'Use this tool to retrieve the ancestor path and sibling nodes' and provides the use case 'understanding where a term sits in the ontology hierarchy.' It does not mention when not to use it or alternatives, but the context is clear.

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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