skills.rest
Hung-3008
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metabolomics-workbench-database

Query Metabolomics Workbench compounds, studies, RefMet, and m/z via REST API.

1|Updated Mar 4, 2026
Search Tags:#data#metabolomics#study#rest-api#refmet#metabolite#mw-rest
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill metabolomics-workbench-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill metabolomics-workbench-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Metabolomics researchers often struggle to programmatically access and integrate data from the Metabolomics Workbench. This Skill provides a REST API-driven gateway to query compounds, studies, RefMet classifications, and MS/NMR data, enabling seamless integration into analysis pipelines.

Core Features & Use Cases

  • Query metabolite structures, identifiers, and cross-references
  • Retrieve study metadata, experimental data, and mwTab format
  • Standardize names with RefMet and support mass-spectrometry searches
  • Filter studies by analytical method, organism, tissue, and disease
  • Access gene and protein associations for metabolic pathway context

Quick Start

Query a metabolite, retrieve study data, and search by m/z using the REST API.

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 metabolomics study metadata and compound data programmatically?▼

You can query metabolomics study metadata and compound data by sending requests to the Metabolomics Workbench REST API endpoints, which return structured json or txt output for compounds, studies, and mwTab data.

Can I search metabolites by m/z value and filter studies by organism or disease?▼

Yes, mass-spectrometry searches by m/z are supported, and you can filter metabolomics studies by analytical method, organism, tissue, and disease using specific REST API input parameters.

What is RefMet nomenclature and how do I standardize metabolite names with it?▼

RefMet is a standardized nomenclature system provided by the Metabolomics Workbench API that allows you to normalize metabolite names and retrieve cross-references for consistent data integration across diverse studies.

How do I retrieve mwTab format experimental data and gene associations for metabolic pathways?▼

You can retrieve mwTab format experimental data and access gene and protein associations for metabolic pathway context by calling the respective MW REST API endpoints with the correct study identifiers and output formats.

Does the Metabolomics Workbench REST API require authentication or specific dependencies to use?▼

No specific dependencies or authentication are required to start querying the Metabolomics Workbench REST API, as the Skill operates independently with enforced endpoints and practical examples for reliable integration.

What are the limitations when querying cross-references and MS or NMR data through the REST API?▼

The REST API enforces specific endpoints, input parameters, and output formats (json/txt), meaning queries must strictly match available Metabolomics Workbench data structures for compound, study, and RefMet retrieval.

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