skills.rest
JosephWoodall
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metabolomics-workbench-database

Query the Metabolomics Workbench REST API for metabolite, study, and RefMet data.

1|Updated Mar 19, 2026
Search Tags:#api#rest#metabolomics#refmet#mwrestapi#study-data#mz-search
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill metabolomics-workbench-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill metabolomics-workbench-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The Metabolomics Workbench REST API provides programmatic access to thousands of metabolomics studies, enabling researchers to retrieve study metadata, metabolite data, RefMet nomenclature, and mass spectrometry results in a consistent, machine-readable format.

Core Features & Use Cases

  • Query studies by metabolite, investigator, or metadata to assemble a comprehensive view of public metabolomics data.
  • Retrieve compound and RefMet data, MWTab exports, and experimental factors for downstream analysis and biomarker discovery.
  • Use programmatic queries to standardize metabolite names, perform m/z searches, and integrate MW data into analytical pipelines.

Quick Start

Use a single REST call to fetch study or compound data for a metabolite of interest.

Frequently Asked Questions about metabolomics-workbench-database

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

FAQPage Schema
How do I retrieve metabolomics study data via the Metabolomics Workbench REST API?▼

Yes, you can query the Metabolomics Workbench REST API to cross-reference compounds with study metadata and retrieve RefMet nomenclature. This standardizes metabolite names for biomarker discovery pipelines.

Can I perform m/z searches and retrieve RefMet data using MW REST API?▼

The API supports multiple data contexts including study, compound, refmet, metstat, gene, protein, and moverz. You access these contexts through structured REST calls to retrieve specific metabolomics data types.

How do I export metabolomics data in MWTab format for an analytical pipeline?▼

You can export metabolomics data in MWTab format by querying the Metabolomics Workbench REST API. The API supports MWTab exports alongside structured JSON outputs, enabling integration into downstream analytical pipelines and biomarker discovery workflows.

Does the Metabolomics Workbench API support queries by investigator or study metadata?▼

The API provides consistent JSON and MWTab outputs to support downstream analysis and biomarker discovery. It standardizes metabolite names via RefMet and integrates metabolomics data into analytical pipelines.

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