Hmdb Database

This gives Claude access to HMDB, the Human Metabolome Database with 220,000+ metabolite entries. It's built for metabolomics research, biomarker discovery, and compound identification tasks. You can search by metabolite name, structure, or mass spec data, then pull detailed info like chemical properties, biological pathways, disease associations, and reference spectra. The database doesn't have a public API, so this skill handles web searches and helps you work with downloadable XML or CSV datasets. One thing to note: HMDB is comprehensive but updated periodically, so version tracking matters if you're publishing results. Free for academic use, but commercial work needs permission from the University of Alberta team.

skills.sh installs: 222
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill hmdb-database --agent claude-code

Installs into .claude/skills of the current project.

Files

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)