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reactome-mcp

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by reactome

reactome_pathway_contained_events

Retrieve all sub-pathways and reactions contained within a specified pathway using its stable ID or database ID.

Instructions

Get all events (sub-pathways and reactions) contained within a pathway.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesPathway stable ID or database ID
Behavior2/5

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

With no annotations, the description carries the full burden for behavioral disclosure. It does not clarify whether 'contained' means direct children or all descendants, how events are structured in the response, or any limitations such as return size or error conditions. The description adds minimal context beyond the tool's basic purpose.

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 a single concise sentence that is front-loaded with the action and resource. It contains no wasted words and is appropriately sized for the tool's simplicity.

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

Completeness3/5

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, the description is adequate but not fully complete. It lacks explicit clarification of 'contained' (direct vs. all descendants) and the return structure, especially since there is no output schema. The ambiguity between this and reactome_events_hierarchy leaves room for misinterpretation.

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% for the single parameter 'id', which is described as 'Pathway stable ID or database ID'. The description adds no additional semantic detail about the parameter, such as accepted formats or examples, so it meets the neutral baseline for high schema coverage.

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 a specific verb ('Get') and resource ('events contained within a pathway'), and defines events as sub-pathways and reactions. This clearly distinguishes it from sibling tools like reactome_get_pathway and reactome_pathway_ancestors.

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?

The phrase 'contained within a pathway' implies the tool is used to retrieve child events of a pathway, but there is no explicit guidance on when to use this over siblings like reactome_events_hierarchy or reactome_pathway_ancestors. 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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