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hmdb-database

Search HMDB metabolite data by name, ID, or structure.

1|Updated Mar 11, 2026
Search Tags:#metabolomics#metabolites#pathways#databases#hmdb#spectra#biomarkers
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill hmdb-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/hmdb-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill hmdb-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

HMDB provides a centralized resource for metabolite data, enabling researchers to identify compounds, discover biomarkers, and place results in the context of metabolic pathways.

Core Features & Use Cases

  • Text-based and structure-based searches by metabolite name, HMDB ID, SMILES, InChI, or synonyms.
  • Retrieve chemical properties, spectral data (NMR, MS), concentrations, and cross-references (KEGG, PubChem, SMPDB).
  • Use Case: In a metabolomics study, quickly pull a metabolite’s properties, spectra, normal concentrations, and implicated pathways to support validation and interpretation.

Quick Start

Ask HMDB for a metabolite by name or HMDB ID and retrieve its properties, spectra, and pathway context

Frequently Asked Questions about hmdb-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search for metabolite data using HMDB ID or chemical structure?▼

Search HMDB by metabolite name, HMDB ID, SMILES, or InChI to retrieve comprehensive chemical properties, spectral data, normal concentrations, and cross-references for metabolomics research.

What metabolite spectra and concentration data can I retrieve for biomarker discovery?▼

Retrieve NMR and MS spectral data alongside normal concentration values and pathway annotations from HMDB to support biomarker discovery workflows and clinical chemistry validation.

Does HMDB metabolite data include cross-references to KEGG and PubChem pathways?▼

HMDB metabolite data includes cross-references to KEGG, PubChem, and SMPDB to place compounds in the context of metabolic pathways for pathway analysis and interpretation.

Can I download HMDB metabolite datasets in CSV or XML formats for pathway analysis?▼

Download HMDB metabolite datasets in XML or CSV formats to enable offline pathway analysis, biomarker discovery, and integration with local metabolomics workflows.

What's the best way to identify metabolites from mass spectrometry data using HMDB?▼

Use HMDB structure-based searches and MS spectral data integration to identify metabolites from mass spectrometry data by retrieving matching chemical properties and implicated pathways for validation.

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