HMDB Database — Local XML Access

Overview

Query the Human Metabolome Database (HMDB, 220,000+ metabolite entries) by parsing locally downloaded XML with Python's ElementTree. Covers metabolite lookup, chemical properties, biological context (pathways, enzymes, biofluids), disease/biomarker associations, spectral data for metabolite identification, and cross-database ID mapping to KEGG, PubChem, ChEBI, and DrugBank.

When to Use

• Looking up metabolite information (description, chemical class, cellular location) by HMDB ID or name
• Retrieving chemical properties (molecular weight, formula, SMILES, InChI, logP, PSA) for metabolomics analysis
• Finding pathway associations and enzyme links for a set of metabolites
• Identifying biofluid/tissue locations of metabolites (blood, urine, CSF, saliva)
• Querying disease associations and normal/abnormal concentration ranges for biomarker discovery
• Extracting NMR or MS spectral peak lists for metabolite identification
• Mapping HMDB IDs to KEGG, PubChem, ChEBI, DrugBank, or other databases
• For drug-specific data (interactions, targets, pharmacology) use drugbank-database-access instead
• For live compound property queries without downloading use pubchem-compound-search instead

Prerequisites