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hmdb-database

Retrieve metabolite data from HMDB by name, ID, or structure.

1|Updated Mar 4, 2026
Search Tags:#metabolomics#pathways#hmdb#spectra#biomarkers#metabolite-search#data-downloads
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill hmdb-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/hmdb-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill hmdb-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

HMDB provides a comprehensive resource for metabolite data, enabling researchers to quickly access chemical properties, biological context, and clinical relevance to support metabolomics workflows.

Core Features & Use Cases

  • Web-based search: text, structure, and spectral queries to locate metabolites and related data.
  • Comprehensive metabolite data: chemical properties, pathways, enzymes, and clinical information for each entry.
  • Data downloads & programmatic access: formats like XML, SDF, FASTA, CSV/TSV for offline analysis and integration; R/Bioconductor and local XML/CSV parsing as alternatives.

Quick Start

Search HMDB for a metabolite by name or HMDB ID and review its chemical properties, pathways, and spectra.

Frequently Asked Questions about hmdb-database

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

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

HMDB metabolite search supports queries by metabolite name, HMDB ID, or chemical structure. It returns comprehensive chemical properties, biological context, pathways, and spectra for each matched entry.

What metabolite data formats are available for download from HMDB for offline analysis?▼

HMDB data downloads are available in XML, SDF, FASTA, and CSV/TSV formats. These support offline metabolomics analysis, local parsing, and dataset integration.

Can I access HMDB metabolomics data programmatically using R packages?▼

Yes, programmatic access to HMDB metabolomics data is supported through R packages and Bioconductor, or by local parsing of downloaded XML and CSV files for metabolomics research.

What biological and clinical information does HMDB provide for each metabolite entry?▼

HMDB metabolite entries include chemical properties, biological context, associated pathways, enzymes, and clinical relevance information to support metabolomics research.

Does HMDB support spectral queries for identifying metabolites and biomarkers?▼

Yes, HMDB supports spectral queries alongside text and structure searches to locate metabolites. This enables identification of metabolites and biomarkers using spectral data.

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