A connection to Reactome, a database that records biological pathways—the chains of reactions and interactions inside living cells.

It is for looking up biological pathways and related data in software workflows.

It gives a coding agent access to pathway information without manually searching the database.

reactome — MCP server by pipeworx-io

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods

npx agentmods add mcp/pipeworx-io/mcp-reactome/reactome

Clone the repo

git clone --depth 1 https://github.com/pipeworx-io/mcp-reactome

Made for: Claude Code, Codex, Cursor.

Per session not measured What this adds to a session before it is invoked.

When invoked not measured Not applicable: nothing here is loaded into a session.

Security scan A 0 findings. Scan, not verified.

Origin 80% copy Near-identical to another mod in the catalogue.

Security

Grade A, and why

reactome scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

80% identical to geoboundaries — 4 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

server.json · 6 lines

What it actually says

{
  "reactome": {
    "url": "https://gateway.pipeworx.io/reactome/mcp",
    "type": "streamable-http"
  }
}

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2d ago First seen · 6 lines scan A 2ddbf2918471

Subscribe to this mod's changes

reactome is an MCP server published in the GitHub repository pipeworx-io/mcp-reactome (0 stars, last pushed 7d ago), licensed MIT. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. It is 80% identical to geoboundaries, differing in 4 lines, and is treated as a copy.

Reactome Scientific mcp mcp-server model-context-protocol pipeworx

reactome

Getting it into your agent

Grade A, and why

Nothing flagged

This is a copy

What it actually says

What this file has done since we first saw it

Other mcp servers, from other repositories

arcgis-charlotte

stat-ee

owid

emdb

regulatory-catalysts

bioregistry