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Metabolomics Workbench Database

Listed
jackspace·vlatest·database·MIT

Access and query Jackspace's curated metabolomics data, workflows, and analyses for rapid research insights.

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 jackspace/claudeskillz --skill metabolomics-workbench-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

jackspace

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: www.metabolomicsworkbench.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

    www.metabolomicsworkbench.orgundeclared

    What it found (3 of 28)

    • skills/scientific-db-metabolomics-workbench-database/SKILL.md:33contacts www.metabolomicsworkbench.org
      response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
    • skills/scientific-db-metabolomics-workbench-database/SKILL.md:36contacts www.metabolomicsworkbench.org
      response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png')
    • skills/scientific-db-metabolomics-workbench-database/SKILL.md:39contacts www.metabolomicsworkbench.org
      response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json')

  • 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 jackspace/claudeskillz at aef4e299d1.

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

Commit
aef4e299d1
Manifest
skills/scientific-db-metabolomics-workbench-database/SKILL.md
Scanned
2 files, 244 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 the Metabolomics Workbench database, a public repository of metabolomics data. It allows you to query and retrieve experimental datasets, sample metadata, and associated analytical results related to metabolic profiling experiments. The database contains diverse data types including LC-MS, GC-MS, NMR, and others.

When to use it

  • Literature Review: Quickly find relevant metabolomics datasets for a specific research question or disease area.
  • Data Integration: Combine Metabolomics Workbench data with your own experimental results for comparative analysis.
  • Reproducibility Checks: Verify the availability of raw data and analytical pipelines used in published studies.
  • Secondary Data Analysis: Explore existing metabolomics datasets to identify novel biomarkers or metabolic pathways.

Key capabilities

  • Dataset search by keyword, experiment type, organism, and other criteria.
  • Access to sample metadata including experimental conditions and clinical information.
  • Retrieval of raw data files (subject to availability and user permissions).
  • Querying for specific analytical results and processing parameters.

Example prompts

  • "Find metabolomics datasets related to Alzheimer's disease."
  • "Show me datasets from E. coli using LC-MS analysis."
  • "Retrieve the raw data files for experiment ID HMDB000010."

Tips & gotchas

  • Familiarity with Metabolomics Workbench’s data structure and search syntax will improve query results.
  • Data availability may be limited depending on user permissions and dataset restrictions.