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hmdb-database

Query HMDB by name, ID, or SMILES/InChI to retrieve chemical, biological, spectral data and cross-links.

6|Updated Dec 30, 2025
Search Tags:#metabolites#pathways#hmdb#spectra#biomarkers#data-retrieval
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill hmdb-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/hmdb-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill hmdb-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers often need rapid, structured access to HMDB data. This Skill provides a direct means to search HMDB by name, ID, or chemical structure and retrieve comprehensive chemical, biological, and spectral information to support identification, biomarker discovery, and pathway analysis.

Core Features & Use Cases

  • Efficient metabolite lookup by HMDB accession, name, synonyms, SMILES or InChI
  • Retrieve multi-field data layers: chemical properties, biological context, disease associations, spectra, and cross-database links
  • Use cases include metabolite identification in untargeted studies, biomarker validation, and literature-supported data assembly for reports

Quick Start

Use HMDB to look up a metabolite (e.g., glucose or HMDB0000122) and pull its chemical, spectral, and pathway data for downstream analysis.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I retrieve HMDB metabolite data by name or chemical structure?▼

Retrieve HMDB metabolite data by searching the database using the metabolite name, HMDB accession ID, synonyms, SMILES, or InChI string to access comprehensive chemical and biological information.

What biological and spectral information can I get from an HMDB metabolite lookup?▼

An HMDB metabolite lookup returns multi-field data layers including chemical properties, biological context, disease associations, spectral data, and cross-database links for integration into analysis pipelines.

Can I use HMDB data retrieval for biomarker discovery and pathway analysis?▼

HMDB data retrieval supports biomarker discovery, clinical chemistry, and pathway analysis by enabling quick metabolite lookups and aggregating comprehensive data across chemical, biological, and spectral fields.

How do I identify metabolites in untargeted metabolomics studies using HMDB?▼

Identify metabolites in untargeted metabolomics studies by querying HMDB with chemical structures or identifiers to retrieve matching chemical properties and spectral data for validation.

What's the best way to access cross-database links for metabolites?▼

Access cross-database links by performing a metabolite lookup in HMDB, which retrieves comprehensive data layers that include references for integration into downstream analysis pipelines.

Does HMDB data retrieval support programmatic access for metabolomics research?▼

HMDB data retrieval satisfies programmatic data access requirements, supporting metabolomics research by enabling structured searches by multiple identifiers and returning comprehensive chemical, biological, and spectral information.

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