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reactome-mcp

reactome-mcp

by tc2fh
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

download_export

Download Reactome exports (SBML, SBGN, PDF, diagram images) to local disk and return the absolute file path, avoiding large payloads in chat.

Instructions

Stream a Reactome export to local disk and return the absolute path.

Use this for any non-trivial payload (full SBML/SBGN, PDF documents, large
diagram images) instead of pulling it into the chat.

Args:
    stable_id: Event/diagram/reaction stable id; for `kind="fireworks"` a
        species name or taxId.
    kind: One of "event" (sbml/sbgn), "diagram" (png/jpg/gif/svg),
        "document" (pdf), "reaction" (png/jpg/gif/svg), or "fireworks"
        (png/jpg/gif/svg, species-level overview).
    ext: File extension valid for the chosen `kind`.
    save_dir: Local directory to save into; created if absent.

Returns:
    Absolute path to the saved file, or a string starting with "ERROR:".

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": "download_export"
  }
}

Input Schema

NameRequiredDescriptionDefault
extNosbml
kindNoevent
save_dirNo./reactome_downloads
stable_idYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.5/5.0
Behavior4/5

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

With no annotations, the description carries the full burden. It discloses the write-to-disk side effect, directory creation ('created if absent'), and the error return format ('ERROR:'). It does not mention overwrite behavior or file naming, but covers the main behavioral traits.

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 front-loaded with the purpose, followed by usage guidance, then a structured Args list and Returns. It is concise and every sentence earns its place, with no wasted words.

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 download tool with 4 parameters and no annotations, the description is thorough: purpose, usage, parameter semantics, and return format. Minor gaps like overwrite behavior and exact file naming remain, but it is essentially complete.

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%, but the Args section thoroughly explains each parameter: stable_id with fireworks naming, kind with valid values, ext validity for the chosen kind, and save_dir creation. This adds substantial meaning beyond the schema's titles/defaults.

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 states 'Stream a Reactome export to local disk and return the absolute path', which is a specific verb+resource+outcome. It distinguishes from siblings by mentioning use for non-trivial payloads and listing format types (SBML/SBGN, PDF, diagram images), clearly setting it apart from tools that return content directly.

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

Usage Guidelines4/5

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

It explicitly says 'Use this for any non-trivial payload ... instead of pulling it into the chat', providing clear when-to-use context. However, it does not name specific alternative tools or state when-not-to-use, so it stops short of full alternatives/ exclusions guidance.

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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