hmdb-database
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-accessinstead - For live compound property queries without downloading use
pubchem-compound-searchinstead
Prerequisites
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