metabolomics-workbench-database

Query NIH Metabolomics Workbench studies, metabolites, and RefMet nomenclature via REST API.

Updated Aug 23, 2026

Search Tags:#metabolomics #REST API #RefMet #metabolite data #mwtab #pubchem

Ready to run

npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill metabolomics-workbench-database-dakesan

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Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill metabolomics-workbench-database-dakesan

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes references (resource) components.

## What problem does it solve? This Skill provides programmatic access to NIH Metabolomics Workbench data (4,200+ studies, RefMet nomenclature, MS/NMR data) via REST API, reducing manual data gathering and standardization overhead for metabolomics research.

## Core Features & Use Cases

Query metabolite structures, metabolites and study metadata, RefMet nomenclature, and MS/NMR results through a unified REST interface.
Retrieve complete study information, download mwTab outputs, and perform cross-database metabolite standardization.
Use-case example: find all studies mentioning a metabolite, standardize its name with RefMet, and fetch associated mwTab data for downstream biomarker analyses.

Quick Start

Example: Retrieve compound data by PubChem CID using Metabolomics Workbench REST: https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json