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LeonChaoX
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hmdb-database

Retrieve metabolite records from the Human Metabolome Database by identifiers and biological context.

783|65|Updated Feb 27, 2026
Search Tags:#metabolomics#pathway analysis#biomarker discovery#hmdb#spectral matching#chemical identifiers
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill hmdb-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/LeonChaoX/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/LeonChaoX/qinyan-academic-skills --skill hmdb-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill helps researchers quickly locate human metabolite information needed for metabolomics, biomarker discovery, and metabolite identification, reducing time spent manually searching across scattered chemical and clinical resources.

Core Features & Use Cases

  • Metabolite discovery by multiple identifiers: Search HMDB by metabolite name, synonym, HMDB ID, chemical identifiers, and biological specimen/disease context.
  • Structure and spectral assisted identification: Use structure-based querying (SMILES/InChI, ChemQuery) and support spectrum-based matching workflows (NMR/MS and LC-MS/GC-MS references).
  • Retrieve actionable biological and analytical fields: Extract chemical properties, pathway/reaction context, clinical concentration ranges, biomarker associations, and linked database cross-references.

Quick Start

Use the hmdb-database skill to retrieve key HMDB fields for a candidate metabolite (e.g., provide an HMDB ID or name) and return chemical properties, clinical concentration context, pathway associations, and available NMR/MS reference 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 metabolite records from the Human Metabolome Database using a name or HMDB ID?▼

To retrieve metabolite records from HMDB, provide the metabolite name, HMDB ID, or chemical identifiers. The system extracts chemical properties, clinical concentration ranges, pathway associations, and available spectral data.

Can I use SMILES or InChI structure strings for metabolite identification?▼

Yes, structure-based querying is supported for metabolite identification. You can input SMILES or InChI strings to locate matching metabolites and retrieve their corresponding biological, clinical, and analytical reference fields.

How does HMDB support biomarker discovery and disease association lookup?▼

Biomarker discovery is supported by querying disease associations and clinical concentration ranges. This allows researchers to identify metabolites linked to specific conditions and extract actionable biological context for downstream analysis.

What is the best way to match experimental NMR or MS spectra against HMDB reference data?▼

Spectral matching workflows are supported by retrieving available NMR and MS reference data. You extract these spectral fields for candidate metabolites to compare against your experimental LC-MS, GC-MS, or NMR results.

Do I need to download local HMDB datasets to access pathway and reaction context?▼

Accessing pathway and reaction context requires connecting to HMDB web resources or using locally downloaded HMDB datasets. This setup ensures you can retrieve linked reaction fields and output clear HMDB citations.

What specific chemical and clinical data fields can I extract for metabolomics workflows?▼

For metabolomics workflows, you can extract chemical properties, clinical concentration context, pathway associations, and NMR/MS reference data. Linked database cross-references are also available for downstream research use.

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