hmdb-database

Search and retrieve metabolite data from the Human Metabolome Database.

8|Updated Nov 19, 2025

Search Tags:#metabolomics #pathway analysis #chemical properties #hmdb #biomarker #metabolite

Ready to run

npx skills add https://github.com/sanand0/scientific-research --skill hmdb-database-sanand0

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/hmdb-database
Command: npx skills add https://github.com/sanand0/scientific-research --skill hmdb-database-sanand0

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides access to the Human Metabolome Database (HMDB), enabling researchers to find detailed information about metabolites, their properties, and their roles in human health and disease.

Core Features & Use Cases

Metabolite Search: Search for metabolites by name, ID, or chemical structure.
Data Retrieval: Access chemical properties, biological context, clinical data, and spectral information for over 220,000 metabolites.
Use Case: Identify unknown compounds in a metabolomics experiment by matching their mass spectrometry data against HMDB's spectral library.

Quick Start

Search the HMDB database for metabolites associated with the disease 'diabetes'.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema

How do I search the Human Metabolome Database for disease biomarkers?▼

You can search the Human Metabolome Database (HMDB) by disease name, metabolite name, or ID to retrieve clinical data and identify potential disease biomarkers. This facilitates targeted metabolomics research by linking specific metabolic profiles to human health conditions.

Can I identify unknown compounds using mass spectrometry data in HMDB?▼

Yes, you can identify unknown compounds by matching your mass spectrometry data against HMDB's spectral information library. This process leverages the database's extensive spectral records to accurately annotate and identify metabolites in your experimental samples.

What metabolite chemical properties and biological pathways can I retrieve from HMDB?▼

You can retrieve comprehensive chemical properties, biological pathway associations, and clinical context for over 220,000 metabolites from HMDB. This data supports pathway analysis and helps map metabolic mechanisms within biological systems.

Does the HMDB metabolomics database require external dependencies for pathway analysis?▼

No dependencies are required to access the HMDB metabolomics database for pathway analysis. The Skill provides direct, programmatic access to comprehensive metabolite data, allowing you to query biological pathways and chemical properties without external library installations.

What is the best way to retrieve biological context for over 220,000 metabolites?▼

The best way to retrieve biological context for these metabolites is querying the Human Metabolome Database directly. It provides programmatic access to detailed clinical data, biological pathways, and spectral information for comprehensive biomarker discovery and metabolomics research.

When should I not use HMDB for metabolite identification?▼

You should not use HMDB for metabolite identification if your research involves non-human organisms, as the database is specifically curated for human metabolism. It is tailored for human metabolomics, biomarker discovery, and human pathway analysis.