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Tooluniverse Metabolomics

Checked
mims-harvard·vlatest·other·Apache-2.0

Analyzes complex metabolic data to identify biomarkers and understand biological pathways, aiding in research & diagnostics.

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 mims-harvard/tooluniverse --skill tooluniverse-metabolomics -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

mims-harvard

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 passed all 6 checks. We read its files at one commit and looked for the things that make a skill dangerous to run — not for whether it works.

  • 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 undeclared network calls: passed

    Makes no network calls.

    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.

  • 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 mims-harvard/tooluniverse at f5c37eebeb.

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

Commit
f5c37eebeb
Manifest
skills/tooluniverse-metabolomics/SKILL.md
Scanned
39 files, 4,838 lines
Copies in repo
3 — all of them scanned
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, Tooluniverse Metabolomics, is designed to assist with metabolomics research by identifying metabolites, retrieving study information, and searching relevant databases. It analyzes complex metabolic data to provide structured reports containing annotated metabolite information, study details, and database statistics. The skill follows a four-phase analysis pipeline covering metabolite identification, study retrieval, study search, and database overview.

When to use it

  • When you need to identify or annotate metabolites (e.g., find HMDB IDs or pathways).
  • To retrieve detailed information about metabolomics studies from MetaboLights or Metabolomics Workbench.
  • When searching for metabolomics studies related to a specific keyword or disease.
  • For analyzing metabolite profiles or datasets.
  • To generate comprehensive research reports summarizing metabolomics findings.

Key capabilities

  • Metabolite Identification & Annotation: Identifies metabolites and retrieves information like HMDB IDs, chemical formulas, molecular weights, pathways, and PubChem CIDs.
  • Study Details Retrieval: Retrieves metadata (title, description, organism, status) for studies from MetaboLights and Metabolomics Workbench.
  • Study Search: Searches MetaboLights for studies based on keywords or disease terms.
  • Database Coverage: Integrates with HMDB, MetaboLights, Metabolomics Workbench, and PubChem.

Example prompts

  • "What is the HMDB ID and pathway information for glucose?"
  • "Get study details for MTBLS1"
  • "Find metabolomics studies related to diabetes"
  • "Analyze these metabolites: glucose, lactate, pyruvate"

Tips & gotchas

  • The skill utilizes a four-phase analysis pipeline. Understanding this structure can help interpret the results.
  • If HMDB data is unavailable for a metabolite, the skill will fall back to PubChem.