metabolomics-workbench-database

Query the NIH Metabolomics Workbench REST API for metabolomics data.

1|Updated Mar 12, 2026
One-click install
npx skills add https://github.com/yf8578/clawomics --skill metabolomics-workbench-database-yf8578
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/yf8578/clawomics --skill metabolomics-workbench-database-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the NIH Metabolomics Workbench, enabling users to query vast amounts of metabolomics data, standardize metabolite names, and retrieve study metadata.

Core Features & Use Cases

  • Metabolite Querying: Search for metabolite structures, identifiers, and nomenclature.
  • Study Data Access: Retrieve metadata and experimental results from over 4,200 metabolomics studies.
  • Nomenclature Standardization: Use RefMet to standardize metabolite names.
  • Mass Spectrometry Search: Perform m/z searches for compound identification.
  • Use Case: A researcher needs to find all studies related to "glucose" metabolism in human blood samples analyzed by LC-MS. This Skill can directly query the database to provide relevant study IDs and associated data.

Quick Start

Use the metabolomics-workbench-database skill to find all studies containing the metabolite 'glucose'.

Frequently Asked Questions about metabolomics-workbench-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query NIH metabolomics studies for specific metabolites like glucose?

You can query metabolomics studies by accessing the NIH Metabolomics Workbench REST API to search for metabolites like glucose, retrieving study IDs, metadata, and experimental results from over 4,200 available studies.

Can I standardize metabolite nomenclature using RefMet for biomarker discovery?

Yes, you can standardize metabolite nomenclature by using RefMet through the NIH Metabolomics Workbench API. This normalizes metabolite names and identifiers to support consistent biomarker discovery and bioinformatics analysis.

How do I perform a mass spectrometry m/z search to identify compounds?

Mass spectrometry searches are performed by querying the NIH Metabolomics Workbench API with specific m/z values to identify matching compounds. This facilitates compound identification by matching experimental mass spectrometry data against the database.

Does this metabolomics database API support filtering studies by human blood samples analyzed by LC-MS?

The NIH Metabolomics Workbench REST API supports querying metabolomics data to find studies matching specific experimental conditions like human blood samples analyzed by LC-MS. It retrieves relevant study IDs and associated experimental results.

What is the best way to programmatically access metabolomics study metadata for bioinformatics workflows?

The best way to programmatically access metabolomics study metadata is via the NIH Metabolomics Workbench REST API. It provides programmatic access to retrieve study metadata and experimental results from over 4,200 studies for bioinformatics workflows.

Are there limitations when retrieving experimental results from over 4,200 metabolomics studies?

Limitations depend on the NIH Metabolomics Workbench REST API response times and data availability across the 4,200 studies. While it facilitates retrieving experimental results, study completeness and metadata standardization may vary between individual studies.