hmdb-database

Search the Human Metabolome Database for metabolites by name, ID, or structure.

Updated Mar 15, 2026

Search Tags:#database #metabolomics #HMDB #biomarker #human metabolism #chemical identification

Ready to run

npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill hmdb-database-sagunkayastha

💬 Prompt for ChatGPT / Claude Chat▼

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

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 search and retrieve detailed information about metabolites, their properties, and their roles in human biology and disease.

Core Features & Use Cases

Metabolite Search: Find metabolites by name, ID, or chemical structure.
Data Retrieval: Access chemical properties, biological context, clinical data, and spectral information.
Use Case: A researcher needs to identify unknown compounds detected in a metabolomics study. They can use this Skill to search HMDB by spectral data or chemical properties to find potential matches and gather supporting information.

Quick Start

Search the Human Metabolome 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 specific metabolites?▼

You can search the Human Metabolome Database by entering a metabolite name, HMDB ID, or chemical structure to retrieve comprehensive metabolomic data. This returns detailed chemical, biological, and clinical information for over 220,000 metabolite entries.

What metabolomic data can I retrieve for biomarker discovery research?▼

For biomarker discovery, you can retrieve comprehensive metabolomic data including chemical properties, biological context, clinical data, and spectral information. This supports clinical chemistry research by providing detailed biological and disease context for human metabolism.

How do I identify unknown compounds detected in a metabolomics study?▼

To identify unknown compounds in metabolomics studies, search HMDB using spectral data or chemical properties to find potential matches. This yields supporting information to confirm chemical identification and understand the compound's biological role.

Can I access clinical and spectral information for human metabolism research?▼

Yes, you can access detailed clinical and spectral information for human metabolism research through the database. It provides programmatic retrieval of biological context and chemical properties to support comprehensive metabolomic data analysis.

Does the HMDB database support searching for metabolites related to specific diseases?▼

Yes, the HMDB database supports searching for metabolites related to specific diseases like diabetes. You can query the database to retrieve metabolomic data, exploring the roles of metabolites in human biology and disease pathology.