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hmdb-database

Search HMDB metabolite records by name or ID for chemical properties and spectra data.

21|1|Updated Mar 19, 2026
Search Tags:#metabolomics#pathways#hmdb#spectra#biomarkers#data-download#metabolite-search
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill hmdb-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/hmdb-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill hmdb-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to the Human Metabolome Database for comprehensive metabolite information, enabling researchers to search by name, ID, or structure and retrieve chemical properties, biomarker data, NMR/MS spectra, and pathway context to support metabolomics and identification tasks.

Core Features & Use Cases

  • Web-Based Metabolite Searches: Text, structure, and spectral queries to HMDB.
  • Accessing Metabolite Information: Retrieve chemical identities, properties, biological context, clinical relevance, and cross-database links.
  • Downloadable Datasets & Programmatic Access: Bulk data downloads and programmatic querying options for analysis pipelines.
  • Common Workflows: Metabolite identification, biomarker discovery, and pathway analysis.

Quick Start

Query HMDB for a metabolite by name or HMDB ID to retrieve properties, spectra, and pathway data.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I search HMDB for metabolite data using a name or ID?▼

Search HMDB by metabolite name or HMDB ID to retrieve chemical properties, biological context, and cross-database links. This enables structured access to metabolite identities for metabolomics research and identification tasks.

Can I download bulk metabolomics datasets from HMDB for pipeline analysis?▼

Yes, HMDB supports bulk data downloads and programmatic querying options. You can retrieve downloadable datasets containing chemical properties, spectra, and pathway associations for integration into metabolomics analysis pipelines.

What type of spectral data can I retrieve for metabolite identification?▼

You can retrieve NMR and MS spectra data for metabolites from HMDB. This spectral information supports metabolite identification and biomarker discovery by providing reference spectra for experimental data comparison.

How do I find pathway associations and biomarker data for specific metabolites?▼

Query HMDB by metabolite name or ID to access pathway associations and clinical biomarker data. This retrieves biological context and clinical relevance information to support pathway analysis and biomarker discovery workflows.

Does HMDB provide cross-database links and external IDs for metabolites?▼

Yes, HMDB provides cross-database links and external IDs for retrieved metabolites. This allows researchers to map chemical identities to other databases, expanding access to complementary biological and chemical data.

What's the best way to access chemical properties for metabolomics biomarker discovery?▼

Use HMDB to search metabolites by name, ID, or structure to retrieve comprehensive chemical identities and properties. This provides the chemical data foundation necessary for biomarker discovery and pathway analysis workflows.

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