skills.rest
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metabolomics-workbench-database

Query the Metabolomics Workbench REST API for compounds, studies, and RefMet-standardized metabolite names.

1|Updated Mar 11, 2026
Search Tags:#metabolomics#rest-api#refmet#mw-rest#study-metadata#moverz
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill metabolomics-workbench-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill metabolomics-workbench-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers need reliable, programmatic access to the Metabolomics Workbench REST API to discover studies, query metabolites with RefMet standardization, and retrieve MS/NMR data and m/z results for biomarker discovery.

Core Features & Use Cases

  • Unified REST API access for compounds, studies, RefMet, metstat filters, and moverz searches to support end-to-end metabolomics workflows.
  • Retrieve comprehensive study metadata, experimental factors, and raw mwTab data for reproducible analyses.
  • Standardize metabolite nomenclature with RefMet and cross-reference data across multiple MW contexts for accurate identifications.

Quick Start

Query studies for a metabolite by RefMet, then fetch study metadata and perform an m/z search via MW REST endpoints.

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 compounds from the Metabolomics Workbench REST API?▼

The Skill queries the Metabolomics Workbench REST API to retrieve study metadata, compounds, and experimental factors, handling pagination and returning structured JSON or TXT outputs for downstream analysis.

What is RefMet standardization and how does it work for metabolite nomenclature?▼

RefMet standardization is a process that normalizes metabolite names across multiple Metabolomics Workbench contexts, ensuring accurate cross-referencing and consistent metabolite identifications for biomarker discovery workflows.

Can I perform an m/z search using moverz to find specific MS or NMR data?▼

Yes, you can perform moverz searches via the MW REST API to retrieve MS and NMR data results based on specific m/z values, supporting mass spectrometry data identification and biomarker discovery workflows.

Does the MW REST API support output formats suitable for Python or R scripting?▼

Yes, the MW REST API supports both JSON and TXT output formats, and the Skill structures the retrieved metabolomics data for direct consumption by downstream scripting environments like Python or R.

How do I map genes or proteins to metabolites for biomarker discovery workflows?▼

You can map genes and proteins to metabolites by querying specific MW REST endpoints that cross-reference the data, supporting integrated biomarker discovery and metabolomics analysis workflows.

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