hmdb-database

Search and retrieve metabolite data from the Human Metabolome Database.

Updated Mar 10, 2026
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill hmdb-database-felixboehm
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/hmdb-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill hmdb-database-felixboehm

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 biology and disease.

Core Features & Use Cases

  • Metabolite Information Retrieval: Search for over 220,000 metabolites by name, ID, or structure.
  • Data Access: Retrieve chemical properties, biological pathways, clinical data, and spectral information.
  • Use Case: A researcher needs to identify an unknown compound detected in a metabolomics study. They can use this Skill to search HMDB by its mass spectrometry data or chemical structure to find potential matches and their associated biological context.

Quick Start

Search the HMDB database for metabolites related to '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 metabolite information?

You can search the Human Metabolome Database by metabolite name, HMDB ID, or chemical structure to retrieve data on over 220,000 metabolites. This includes accessing detailed chemical properties, biological pathways, and clinical data.

Can I use mass spectrometry data to identify unknown metabolites in HMDB?

Yes, you can identify unknown compounds by searching HMDB using mass spectrometry data or chemical structure. The database returns potential matches along with their associated biological context for metabolite identification.

What type of biological data can I retrieve for biomarker discovery?

For biomarker discovery, you can retrieve chemical properties, biological pathways, clinical data, and spectral information for metabolites. This comprehensive data helps link chemical identification to human biology and disease contexts.

Does the HMDB database contain clinical data for human metabolism research?

Yes, the HMDB database provides clinical data alongside biological pathways and spectral information for human metabolism research. It enables comprehensive metabolomics studies by linking over 220,000 metabolites to disease contexts.

How do I find metabolites related to a specific disease like diabetes?

You can search the HMDB database directly using disease terms such as 'diabetes' to find related metabolites. This retrieves detailed information on metabolites associated with that specific human biology or disease condition.

What are the limitations of using HMDB for chemical identification?

HMDB focuses on human metabolites and may not cover compounds exclusive to other organisms. While it provides extensive spectral data for chemical identification, search accuracy depends on the availability of matching reference profiles in the database.