metabolomics-workbench-database

# 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:** ```python import requests # Get compound information by PubChem CID response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json') # Download molecular structure as PNG response = requests.get('https://www.metabolomicsworkbench.o...