hmdb-database

# HMDB Database ## Overview The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body. ## When to Use This Skill This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks. ## Database Contents HMDB version 5.0 (current as of 2025) contains: - **220,945 metabolite entries** covering both water-soluble and lipid-soluble compounds - **8,610 protein sequences** for enzymes and transporters involved in metabolism - **130+ data fields per metabolite** including: - Chemical properties (structure, formula, molecular weight, InChI, SMILES) - Clinical data (biomarker associations, diseases, normal/abnormal concentrations) - Biological information (pathways, reactions, locations) - Spectroscopic data (NMR, MS, MS-MS spectra) - External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank) ## Core Capabilities ### 1. Web-Based Metabolite Searches Access HMDB through the web interface at https://www.hmdb.ca/ for: **Text Searches:** - Search by metabolite name, synonym, or identifier (HMDB ID) - Example HMDB IDs: HMDB0000001, HMDB0001234 - Search by disease associations or pathway involvement - Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat) **Structure-Based Searches:** - Use ChemQuery for structure and substructure searches - Sea...