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Juancho032007
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hmdb-database

Search the Human Metabolome Database for metabolite data and download bulk datasets.

Updated Aug 23, 2026
Search Tags:#metabolomics#pathway analysis#biomarker discovery#HMDB#chemical properties#metabolite identification#spectroscopy
One-click install
npx skills add https://github.com/Juancho032007/claude-scientific-skills --skill hmdb-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/Juancho032007/claude-scientific-skills/tree/main/scientific-databases/hmdb-database
Command: npx skills add https://github.com/Juancho032007/claude-scientific-skills --skill hmdb-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Manually sifting through vast metabolomics data for metabolite identification, biomarker discovery, or pathway analysis is laborious and inefficient. This Skill provides structured access to the Human Metabolome Database (HMDB), simplifying complex metabolomics workflows and accelerating your research.

Core Features & Use Cases

  • Comprehensive Metabolite Data: Access chemical properties, biological context, clinical relevance, and spectroscopic data (NMR, MS) for over 220,000 human metabolites.
  • Flexible Search Options: Utilize web-based text, structure (SMILES/InChI), or spectral searches to find compounds of interest.
  • Bulk Data Downloads: Obtain complete datasets in XML, SDF, FASTA, or CSV formats for local programmatic analysis and integration into your pipelines.
  • Use Case: A researcher identifies an unknown peak in a mass spectrometry experiment. Using this skill, they can search HMDB by molecular weight and MS/MS fragmentation pattern to identify potential metabolite candidates and retrieve their associated metabolic pathways and biomarker data.

Quick Start

To search for a metabolite by name on the HMDB website: Go to https://www.hmdb.ca/ and use the search bar to enter "glucose". To download bulk data, visit https://www.hmdb.ca/downloads and select your desired format (e.g., XML for comprehensive data).