skills.rest
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metabolomics-workbench-database

Access Metabolomics Workbench REST endpoints for compounds, studies, and RefMet data.

15|2|Updated Dec 17, 2025
Search Tags:#metabolomics#query#rest-api#refmet#compound-data#study-metadata
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill metabolomics-workbench-database-rubensliv
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill metabolomics-workbench-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers often need programmatic access to large-scale metabolomics data. This skill provides a direct bridge to the NIH Metabolomics Workbench REST API, enabling automated retrieval of metabolite data, study metadata, RefMet nomenclature, and associated resources.

Core Features & Use Cases

  • Access compound and study data from MW REST endpoints (compound, study, refmet, metstat, moverz, gene, protein).
  • Retrieve standardized metabolite nomenclature (RefMet), mwTab-like outputs, and cross-database references for integration into analysis pipelines.
  • Use in workflows to build reproducible metabolomics queries, perform metabolite lookups, and fetch study metadata for meta-analyses.

Quick Start

Query metabolites, studies, and RefMet data from the Metabolomics Workbench REST API to bootstrap analysis.

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 compound data from the Metabolomics Workbench REST API?▼

You query metabolomics compound data by sending programmatic requests to the Metabolomics Workbench REST endpoints, retrieving metabolite information, RefMet nomenclature, and cross-database references for analysis pipelines.

Can I fetch study metadata from the Metabolomics Workbench for meta-analysis?▼

Yes, you can fetch study metadata from the Metabolomics Workbench REST API. The Skill accesses study endpoints to retrieve metadata, supporting automated data retrieval for meta-analyses and reproducible workflows.

What metabolomics data contexts are available through the REST API endpoints?▼

Available metabolomics data contexts include compound, study, refmet, metstat, moverz, gene, and protein endpoints. These cover metabolite data, study metadata, nomenclature, and associated biological contexts.

Does the Metabolomics Workbench API integration require any specific dependencies?▼

No specific dependencies are required to use this integration. The Skill operates independently to bridge programmatic access to the Metabolomics Workbench REST API for fetching compounds, studies, and RefMet data.

What's the best way to integrate cross-database metabolite references into an analysis pipeline?▼

The best way to integrate cross-database metabolite references is querying the RefMet nomenclature endpoints via the Metabolomics Workbench REST API, retrieving standardized names and mwTab-like outputs for pipeline integration.

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