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Reactome Database

Listed
jimmc414·vlatest·database

Access and visualize Reactome pathway data via a user-friendly interface built by jimmc414.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add jimmc414/kosmos --skill reactome-database -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

jimmc414

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 1 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 1 host that is neither well-known infrastructure nor declared in the skill's frontmatter: reactome.org.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    reactome.orgundeclared

    What it found (3 of 11)

    • kosmos-claude-scientific-skills/scientific-skills/reactome-database/reactome-database/SKILL.md:72contacts reactome.org
      response = requests.get("https://reactome.org/ContentService/data/database/version")
    • kosmos-claude-scientific-skills/scientific-skills/reactome-database/reactome-database/SKILL.md:82contacts reactome.org
      response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")
    • kosmos-claude-scientific-skills/scientific-skills/reactome-database/reactome-database/SKILL.md:144contacts reactome.org
      response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • No pipe-to-shell installers: passed

    No pipe-to-shell or download-and-run installers.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

  • Pinned to a commit: passed

    Scanned jimmc414/kosmos at 6cfe7f690d.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
6cfe7f690d
Manifest
kosmos-claude-scientific-skills/scientific-skills/reactome-database/reactome-database/SKILL.md
Scanned
3 files, 940 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill provides access to and querying capabilities of the Reactome Pathway Database. It allows users to retrieve information about biological pathways, genes, proteins, and their relationships within those pathways. The database is a manually curated resource focused on human biology but includes data from other organisms as well.

When to use it

  • Research: Investigate specific biological pathways involved in a disease or process.
  • Drug Discovery: Identify potential drug targets by analyzing pathway components and interactions.
  • Education: Visualize and understand complex biological processes for students or researchers.
  • Data Integration: Enrich existing datasets with Reactome pathway annotations.

Key capabilities

  • Pathway search
  • Gene/Protein search
  • Relationship retrieval within pathways
  • Access to curated biological data

Example prompts

  • "Show me the Reactome pathways involved in apoptosis."
  • "What genes are associated with the 'PI3K/AKT/mTOR signaling pathway'?"
  • "Retrieve all proteins that interact with TP53 according to Reactome."

Tips & gotchas

The Reactome database is extensive; be specific with your queries to narrow down results. Understanding basic biological terminology will improve the quality of your interactions with this skill.