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metabolomics-workbench-database

Query NIH Metabolomics Workbench REST API for studies, metabolites, and RefMet data.

6|Updated Dec 30, 2025
Search Tags:#metabolomics#rest-api#data-access#refmet#study-metadata#moverz
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill metabolomics-workbench-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill metabolomics-workbench-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

NIH Metabolomics Workbench data is dispersed across multiple endpoints and formats, making programmatic discovery, retrieval, and cross-referencing slow and error-prone. This skill provides a unified REST API interface to discover, retrieve, and correlate metabolite data, study metadata, RefMet nomenclature, and MS/NMR results for accelerated biomarker discovery and integration workflows.

Core Features & Use Cases

  • Query metabolite structures, study metadata, and RefMet nomenclature across thousands of studies using standardized REST endpoints.
  • Perform mass-spectral searches (moverz) and access mwTab-formatted study data for seamless downstream analysis.
  • Retrieve complete study data, associated factors, and cross-reference gene/protein information for integrative analyses.

Quick Start

Query the REST API to retrieve studies containing metabolite data by RefMet name.

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 metadata from the NIH Metabolomics Workbench REST API?▼

You can retrieve metabolomics study metadata by querying the NIH Metabolomics Workbench REST API using the study endpoint, which returns structured JSON or TXT outputs containing study details and associated factors.

What is RefMet nomenclature and how can I query it for metabolite data?▼

RefMet is a standardized nomenclature system for metabolites. You can query the refmet API endpoint to cross-reference metabolite structures and names across thousands of metabolomics studies for consistent biomarker discovery.

Can I perform mass spectrometry searches against the Metabolomics Workbench database?▼

Yes, you can perform mass spectrometry searches using the moverz API endpoint, which allows you to query metabolomics data by mass-to-charge ratio and retrieve matching MS/NMR results in JSON or TXT format.

Does the Metabolomics Workbench REST API support cross-referencing metabolite data with gene and protein information?▼

Yes, the REST API supports cross-referencing metabolite data with gene and protein information, enabling integrative analyses for workflows that require correlating metabolomics studies with broader biological data.

What output formats are available when querying metabolomics data from the Metabolomics Workbench API?▼

The Metabolomics Workbench REST API returns data in either JSON or TXT formats, including mwTab-formatted study data, allowing seamless downstream analysis and integration into various data pipelines.

How many metabolomics studies are accessible through the Metabolomics Workbench REST API?▼

The Metabolomics Workbench REST API provides access to over 4,000 metabolomics studies, allowing you to query compound data, study metadata, RefMet nomenclature, and mass spectrometry results across a large research dataset.

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