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hmdb-database

Query HMDB by ID, name, or synonyms to retrieve metabolite records.

48|6|Updated Mar 9, 2026
Search Tags:#metabolomics#metabolites#pathways#hmdb#spectra#biomarkers#biochemical-data
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill hmdb-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/hmdb-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill hmdb-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

HMDB is a comprehensive resource for detailed information on human metabolites, enabling researchers to quickly access structure, properties, spectra, pathways, and biomarker data to support metabolomics and clinical studies.

Core Features & Use Cases

  • Web-based searches by HMDB ID, name, synonyms, or structure to retrieve comprehensive metabolite data
  • Access chemical properties, spectra (NMR, MS), pathways, disease associations, and cross-database links
  • Use case: identify a metabolite from a candidate list by comparing structure and spectral data to HMDB entries

Quick Start

Look up a metabolite by HMDB ID or name and retrieve its core properties and spectral data.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I retrieve detailed biochemical data for a specific metabolite using HMDB?▼

To retrieve HMDB biochemical data, query the database by metabolite ID, name, or synonyms. This returns comprehensive records including chemical properties, structures, spectra, pathways, and disease associations for metabolomics research.

Can I find NMR and MS spectra for human metabolites to support biomarker discovery?▼

Yes, querying HMDB metabolite records provides access to detailed NMR and MS spectra. Researchers use this spectral data alongside chemical properties to identify metabolites and validate biomarker discovery workflows.

What is the best way to identify a metabolite from a candidate list using biochemical data?▼

The best way to identify a candidate metabolite is to query HMDB by name or synonyms. You can then compare the retrieved chemical structures, properties, and spectral data against your experimental observations for accurate identification.

Does HMDB provide disease associations and pathway data for clinical metabolomics studies?▼

HMDB provides disease associations and pathway data within its metabolite records. Querying specific metabolites returns these cross-references, directly supporting clinical metabolomics studies and pathway analysis workflows.

How do I find cross-references for human metabolites in other biochemical databases?▼

To find cross-references for human metabolites, query HMDB by ID or name. The retrieved metabolite records include cross-database links, allowing seamless integration of biochemical data into broader research workflows.

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