A local connection to the Reactome database, a resource containing information about biological pathways and reactions. It runs from a Python package and uses a local database name.

Use it for development tasks that need information from a local Reactome database.

It gives an agent a configured way to work with Reactome data instead of setting up that database connection manually.

reactome-db — MCP server by tc2fh/reactome-db-mcp

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.

Clone the repo

git clone --depth 1 https://github.com/tc2fh/reactome-db-mcp

Made for: Claude Code, Codex, Cursor, Gemini CLI, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/mcp/tc2fh/reactome-db-mcp/reactome-db/github.svg)](https://agentmods.dev/mcp/tc2fh/reactome-db-mcp/reactome-db)

Your own site

<a href="https://agentmods.dev/mcp/tc2fh/reactome-db-mcp/reactome-db"><img src="https://agentmods.dev/badge/mcp/tc2fh/reactome-db-mcp/reactome-db/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/mcp/tc2fh/reactome-db-mcp/reactome-db"><img src="https://agentmods.dev/badge/mcp/tc2fh/reactome-db-mcp/reactome-db.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

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. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

reactome-db 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 1mo 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.

.mcp.json · 15 lines

What it actually says

{
  "reactome-db": {
    "type": "stdio",
    "command": "uv",
    "args": [
      "run",
      "--directory",
      "/absolute/path/to/reactome-db-mcp",
      "reactome-db-mcp"
    ],
    "env": {
      "REACTOME_DB_NAME": "reactome_local"
    }
  }
}

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.

1mo ago First seen · 15 lines scan A d795772f5b97

Subscribe to this mod's changes

reactome-db is an MCP server published in the GitHub repository tc2fh/reactome-db-mcp (0 stars, last pushed 4mo 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. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Scientific

reactome-db

Getting it into your agent

Wrote this? Show the measurements

Grade A, and why

Nothing flagged

What it actually says

What this file has done since we first saw it

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