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reactome-db-mcp

reactome-db-mcp

by tc2fh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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get_pathway_events

Retrieve the ordered child events (sub-pathways and reactions) of a pathway using its stable ID or DB_ID.

Instructions

List the ordered child events (sub-pathways & reactions) of a pathway.

Args:
    id: A Pathway stable id ('R-HSA-69278') or numeric DB_ID.

Returns:
    Dict `{pathway_DB_ID, count, events: [{rank, DB_ID, _class,
    _displayName, stable_id}], truncated}`, ordered by `hasEvent_rank`.

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": {
      "id": "<id>"
    },
    "name": "get_pathway_events"
  }
}

Input Schema

NameRequiredDescriptionDefault
idYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.9/5.0
Behavior3/5

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

The description includes ordering by hasEvent_rank and return format, but lacks explicit safety/read-only declaration or truncation details; no annotations to supplement.

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?

Three sentences: purpose, Args, Returns. Front-loaded, no redundant text, efficient for a simple tool.

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?

Covers purpose, parameter, and return structure (including truncation hint). Missing explanation of truncation behavior and any access limitations, but adequate for single-param tool.

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?

Despite 0% schema coverage, the description adds full parameter meaning: stable ID format example and numeric DB_ID, compensating for schema omission.

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 ordered child events (sub-pathways and reactions) of a pathway, distinguishing it from siblings like get_object.

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

Usage Guidelines2/5

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

No guidance on when to use this tool vs alternatives; no mention of when not to use it or context for selection.

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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