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hmdb-database

Query HMDB to identify metabolites via text, structure, and spectral matching.

322|45|Updated Dec 1, 2025
Search Tags:#bioinformatics#metabolomics#biomarker discovery#metabolite identification#chemistry#hmdb#scientific database
One-click install
npx skills add https://github.com/Microck/ordinary-claude-skills --skill hmdb-database-microck
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/Microck/ordinary-claude-skills/tree/main/hmdb-database
Command: npx skills add https://github.com/Microck/ordinary-claude-skills --skill hmdb-database-microck

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires hmdbQuery, and includes references (resource) components.

What problem does it solve?

Accessing and interpreting comprehensive information about human metabolites for metabolomics research, biomarker discovery, or clinical chemistry is complex and often requires navigating disparate data sources. This Skill provides direct access to the Human Metabolome Database (HMDB).

Core Features & Use Cases

  • Extensive Metabolite Information: Search over 220,000 metabolites by name, ID, or structure, retrieving chemical properties, clinical data, and spectroscopic information.
  • Metabolite Identification: Utilize HMDB's spectral matching tools (NMR, MS) to identify unknown compounds from experimental data.
  • Biomarker Discovery & Pathway Analysis: Explore disease associations, normal concentration ranges, and metabolic pathways for clinical relevance.
  • Use Case: If you have an unknown metabolite from a patient sample and its MS spectrum, use this skill to search HMDB for spectral matches, retrieve its chemical properties, and check for known disease associations to aid in identification and biomarker discovery.

Quick Start

Search the HMDB for metabolite HMDB0000001 and retrieve its chemical properties and associated pathways.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I identify an unknown metabolite from MS or NMR spectral data?▼

Metabolite identification uses spectral matching against the Human Metabolome Database. Submit your experimental MS, NMR, or LC-MS spectrum to search HMDB's 220,000+ metabolite records and retrieve chemical properties, structure matches, and disease associations to confirm compound identity.

Can I search HMDB for metabolites by name, ID, or chemical structure?▼

Yes. HMDB supports text queries by metabolite name, ID lookup (e.g., HMDB0000001), and structure or substructure searches. Results return chemical properties, biological context, pathway information, and spectral data across biofluids including urine, serum, and CSF.

What biomarker and disease association data does HMDB provide?▼

HMDB stores disease associations, normal concentration ranges by biofluid, and biomarker data linked to clinical conditions. Query results include pathway and enzyme information, enabling you to assess metabolite relevance for biomarker discovery and clinical chemistry applications.

Does HMDB integrate with other chemical databases for cross-referencing?▼

Yes. HMDB metabolite records include cross-database links to KEGG, PubChem, and ChEBI, enabling seamless integration into analysis pipelines and bulk downloads for downstream research or clinical workflows.

What biofluids and sample types does HMDB metabolite data cover?▼

HMDB covers metabolites detected in urine, serum, cerebrospinal fluid, saliva, and other biofluids. Data includes concentration ranges and spectral information (NMR, MS, LC-MS, GC-MS) for each biofluid type, supporting metabolomics and clinical chemistry research.

What preparation or data format do I need before querying HMDB?▼

Minimal setup required. Provide a metabolite name, HMDB ID, chemical structure, or experimental spectrum (NMR, MS). The Skill handles text queries, structure matching, and spectral comparison without requiring special preprocessing or intermediate format conversion.

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