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metabolomics-workbench-database

Fetch metabolomics study and compound data from the Metabolomics Workbench REST API.

4|1|Updated Jun 18, 2025
Search Tags:#metabolomics#rest-api#data-retrieval#refmet#mw-rest#study-metadata
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill metabolomics-workbench-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill metabolomics-workbench-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The Metabolomics Workbench REST API provides programmatic access to a vast repository of metabolomics studies, compounds, and standardized nomenclature, enabling researchers to discover, retrieve, and integrate data without manual browsing.

Core Features & Use Cases

  • Query metabolite data, study metadata, and RefMet classifications across MW endpoints
  • Retrieve complete study data (summary, factors, and data) and download mwTab representations
  • Leverage API references to understand inputs/outputs and construct robust workflows for data analysis

Quick Start

Query the Metabolomics Workbench REST API to retrieve studies containing a specific metabolite and obtain detailed study data.

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 study metadata from the Metabolomics Workbench REST API?▼

You can retrieve study metadata from the Metabolomics Workbench REST API by querying the specific study endpoints to fetch complete summary information, factors, and data programmatically without manual browsing.

What metabolomics data can I access using the MW REST API?▼

The MW REST API provides access to metabolomics compound data, study metadata, RefMet classifications, and statistical results across multiple endpoints including study, compound, refmet, metstat, and moverz.

How do I get RefMet classifications for metabolites through the Metabolomics Workbench?▼

You can obtain RefMet classifications by querying the dedicated refmet endpoint of the Metabolomics Workbench REST API, which provides standardized nomenclature for discovered metabolites.

Can I download mwTab format representations of metabolomics studies via REST?▼

Yes, the Metabolomics Workbench REST API supports retrieving complete study data and downloading mwTab representations for integration into downstream research workflows.

Does the Metabolomics Workbench API require authentication for data retrieval?▼

The Metabolomics Workbench REST API supports JSON and text outputs for data retrieval, but you must ensure proper authentication if required and respect API rate limits during programmatic access.

What is the best way to integrate metabolomics compound data into a research workflow?▼

The best way to integrate metabolomics compound data is by leveraging the Metabolomics Workbench REST API references to understand inputs and outputs, enabling you to construct robust programmatic workflows for analysis.

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