Agent skill · research science · aiskillstore
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
Why this skill is useful
Provides specific API commands for querying metabolomics data and standardizing nomenclature that the AI wouldn't reliably generate on its own.
What it needs
Requires nih account access. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
Metabolomics Workbench Database Overview The Metabolomics Workbench is a comprehensive NIH Common Fund-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data. It provides programmatic access to over 4,200 processed studies (3,790+ publicly available), standardized metabolite nomenclature through RefMet, and powerful search capabilities across multiple analytical platforms (GC-MS, LC-MS, NMR). When to Use This Skill This skill should be used when querying metabolite structures, accessing study data, standardizing nomenclature, performing mass spectrometry searches, or retrieving gene/protein-metabolite associations through the Metabolomics Workbench REST API. Core Capabilities 1. Querying Metabolite Structures and Data Access comprehensive metabolite information including structures, identifiers, and cross-references to external databases. Key operations: Retrieve compound data by various identifiers (PubChem CID, InChI Key, KEGG ID, HMDB ID, etc.) Download molecular structures as MOL files or PNG images Access standardized compound classifications Cross-reference between different metabolite databases Example queries: 2. Accessing Study Metadata and Experimental Results Query metabolomics studies by various criteria and retrieve complete experimental datasets. Key operations: Search studies by metabolite, institute, investigator, or title Access study summaries, experimental factors, and analysis details Retrieve complete experimental data in various formats Download mwTab format files for complete study information Query untargeted metabolomics data Example queries: 3. Standardizing Metabolite Nomenclature with RefMet Use the RefMet database to standardize metabolite names and access systematic classification across four structural resolution levels. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/metabolomics-workbench-database