hmdb-database

name	hmdb-database
description	Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
license	HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
metadata	{"skill-author":"K-Dense Inc."}
verified	false
lastVerifiedAt	"2026-02-19T05:29:09.098Z"
source	builtin
trust_score	100
provenance_sha	cebf70e7febfb5b6

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
• Search by molecular weight or molecular weight range
• Use SMILES or InChI strings to find compounds

Spectral Searches:

• LC-MS spectral matching
• GC-MS spectral matching
• NMR spectral searches for metabolite identification

Advanced Searches:

• Combine multiple criteria (name, properties, concentration ranges)
• Filter by biological locations or specimen types
• Search by protein/enzyme associations

2. Accessing Metabolite Information

When retrieving metabolite data, HMDB provides:

Chemical Information:

• Systematic name, traditional names, and synonyms
• Chemical formula and molecular weight