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reactome-mcp

reactome-mcp

by tc2fh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

list_pathway_events

Retrieve the complete flattened list of events (sub-pathways and reactions) nested within a pathway by recursing its full sub-tree.

Instructions

List every event (sub-pathway and reaction) contained in a pathway.

Recurses the full sub-tree, so the result is the flattened set of events
beneath the given pathway.

Args:
    stable_id: Pathway stable id, e.g. "R-HSA-69278".

Returns:
    Dict `{count, events}` of Event records (Pathways + ReactionLikeEvents).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "stable_id": "<stable_id>"
    },
    "name": "list_pathway_events"
  }
}

Input Schema

NameRequiredDescriptionDefault
stable_idYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.5/5.0
Behavior5/5

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

With no annotations, the description fully carries the burden of behavioral disclosure. It explicitly discloses the recursion of the full sub-tree and the flattened result set, which are key behavioral traits beyond the basic 'list' 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 efficiently structured: a clear one-sentence summary, followed by Args and Returns sections. Each sentence adds value, and there is no fluff or redundancy.

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 and lack of output schema, the description still specifies the return dictionary format ({count, events}) and the recursive behavior. This provides sufficient context for an agent to invoke the tool and interpret results.

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

Parameters4/5

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

Schema coverage is 0%, but the description compensates by defining stable_id as a 'Pathway stable id' and providing an example ('R-HSA-69278'). This adds semantic meaning beyond the schema's plain string type, though it could offer more detail on acceptable formats.

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 lists every event (sub-pathway and reaction) in a pathway, using a specific verb and resource. It distinguishes itself by noting it recurses the full sub-tree, unlike sibling tools that might handle top-level or ancestor queries.

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 description implies the use case (flatten all events below a pathway) but does not explicitly mention when to prefer it over alternatives or exclude other tools. There is no direct comparison with siblings like get_event_ancestors or get_event_participants.

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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