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reactome-mcp

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by reactome

reactome_complex_subunits

Retrieve all subunits of a biological complex, including components of nested complexes, for pathway analysis.

Instructions

Get all subunits (components) of a complex. Recursively retrieves components of nested complexes.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesComplex stable ID or database ID
Behavior3/5

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

With no annotations provided, the description carries the burden of behavioral disclosure. It adds a valuable detail: recursive retrieval of nested complexes. But it does not describe the return format, any limits, or potential performance implications, leaving notable gaps.

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 concise sentences, front-loaded with the action and resource, and every word adds value. 'Recursively retrieves components of nested complexes' provides key behavior without fluff.

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?

For a simple one-parameter read-only tool with no output schema, the description covers the core purpose and an important behavioral nuance (recursive retrieval). It lacks return value details and usage comparisons, but these are not critical given the tool's simplicity.

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 coverage is 100% with the parameter 'id' described as 'Complex stable ID or database ID'. The description adds no additional semantic detail beyond what the schema already provides, so the baseline score of 3 applies.

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 verb 'Get' and the resource 'subunits (components) of a complex', making the purpose unambiguous. It also differentiates from sibling tools like reactome_complexes_containing by focusing on the complex's own contents, not the complexes that contain an entity.

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?

Usage is implied by the description: use this when you need all subunits of a complex. However, it offers no explicit guidance on when to use it versus similar siblings like reactome_entity_component_of or reactome_participants, and no alternatives or exclusions are mentioned.

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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