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musen-lab

CEDAR MCP Server

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by musen-lab

get_cedar_template

Retrieve a CEDAR metadata template as compact YAML, with optional expansion of ontology branches to list allowed labels or terms.

Instructions

Get a template from the CEDAR repository.

The template is fetched in CEDAR's compact YAML rendering, which is a far cheaper way to read a template than the JSON-LD form: it leaves out provenance and other bookkeeping keys, so it costs fewer tokens.

A field restricted to an ontology branch reports that branch rather than the values it allows. Use expand_branches to list those values, bearing in mind that each branch costs one BioPortal lookup and a template can easily have twenty of them.

Args: template_id: The template ID or full URL from CEDAR repository (e.g., "https://repo.metadatacenter.org/templates/e019284e-48d1-4494-bc83-ddefd28dfbac") expand_branches: How much of each ontology branch to list under permissible_values (default: "none"): "none" reports the branch itself and does no lookups; "labels" lists the allowed labels, which is enough to read a template but carries no IRIs; "terms" lists each label with its IRI, which is what filling in a controlled term field needs, at roughly 1.7x the size of "labels"

Returns: Template data from CEDAR, cleaned and transformed

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
template_idYes
expand_branchesNonone

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

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

With no annotations, the description carries full burden and does an excellent job. It discloses that the output is in compact YAML, that ontology branches are reported as branches unless expanded, that each expansion costs a BioPortal lookup, and that the return data is 'cleaned and transformed.' It even warns that a template 'can easily have twenty' branches, making costs explicit.

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 substantial but perfectly structured: a one-sentence purpose, a rationale for the compact format, a warning about branch costs, and clearly separated parameter explanations. Every sentence adds value, and the section headers (Args, Returns) improve scannability.

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?

Given the tool's moderate complexity (2 params, 1 enum) and the existence of an output schema, the description covers all necessary aspects: purpose, format, cost implications, parameter options, and return transformation. No critical gaps remain.

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 description coverage is 0%, so the description is the sole source of parameter meaning. It explains template_id with an example URL and expand_branches with detailed semantics for each enum value ('none' reports the branch, 'labels' lists labels without IRIs, 'terms' includes IRIs at ~1.7x size).

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 begins with 'Get a template from the CEDAR repository,' clearly identifying the verb, resource, and scope. It also distinguishes this from sibling tools like get_instances_based_on_template by focusing on template retrieval rather than instances, and notes the compact YAML format as a specific feature.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

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

The description explicitly contrasts this with the JSON-LD form, calling it 'far cheaper' and noting it 'leaves out provenance and other bookkeeping keys,' which implies when to choose this over alternatives. It provides direct guidance on when to use expand_branches ('Use expand_branches to list those values, bearing in mind that each branch costs one BioPortal lookup') and explains the trade-offs of each setting.

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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