metabolomics-workbench-database

Topics in the source

• Metabolomics Workbench Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Querying Metabolite Structures and Data
• 2. Accessing Study Metadata and Experimental Results
• 3. Standardizing Metabolite Nomenclature with RefMet
• 4. Performing Mass Spectrometry Searches

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). 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. 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: Query metabolomics studies by various criteria and retrieve complete experimental datasets. Key operations: Search studies by metabolite, ins

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