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hmdb-database

Retrieve HMDB metabolite records with chemical, clinical, and analytical information.

21|2|Updated Dec 8, 2025
Search Tags:#metabolomics#pathway analysis#metabolite identification#hmdb#biomarkers#spectral matching
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill hmdb-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/hmdb-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill hmdb-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

HMDB helps you locate and interpret human small-molecule metabolites, so you can move from metabolomics measurements to concrete chemical IDs, properties, and clinical context without manually stitching together sources.

Core Features & Use Cases

  • Metabolite search by name, ID, or structure to find likely candidates for metabolite identification workflows.
  • Rich metabolite records including chemical identifiers (e.g., SMILES/InChI), physicochemical properties, pathway context, and biomarker/disease associations.
  • Spectra and analytical reference data for supporting LC-MS/GC-MS and NMR-based matching during untargeted or targeted analyses.
  • Versioned bulk datasets guidance for downloading and parsing HMDB exports when you need scalable, repeatable analysis.

Quick Start

Use the hmdb-database skill to retrieve the HMDB record for a specific metabolite and review its chemical properties, pathway links, biomarker associations, and any available spectral references.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I identify metabolites using HMDB records for LC-MS or NMR spectral matching?▼

Metabolite identification using HMDB records involves retrieving chemical, clinical, and analytical metadata to match candidate compounds against your LC-MS or NMR spectral data. The skill extracts spectral references and physicochemical properties to support targeted and untargeted metabolomics workflows.

What is the best way to retrieve physicochemical properties and disease associations for a specific biomarker?▼

Retrieving biomarker data requires querying the HMDB by precise identifier or structure/name concepts. This returns rich metabolite records containing SMILES, InChI, physicochemical properties, pathway context, and disease associations for clinical chemistry interpretation.

Can I use the HMDB database for pathway interpretation in clinical chemistry research?▼

Yes, HMDB records support pathway interpretation by providing metabolite pathway links and biomarker associations. You can extract pathway context and clinical metadata to map small-molecule metabolites to biological processes in clinical chemistry and metabolomics research.

How to download and parse HMDB bulk datasets for scalable metabolomics analysis?▼

HMDB bulk datasets are handled through versioned export downloads. The skill provides guidance on downloading and parsing HMDB exports to enable scalable, repeatable analysis of human metabolite data across metabolite classes.

Does the HMDB database skill work without a public REST API for metabolite searches?▼

Yes, the skill retrieves HMDB metabolite records and related chemical, clinical, and analytical information without requiring a public REST API. It extracts properties, diseases, pathways, and spectra-relevant metadata directly from HMDB content.

What limitations exist when querying HMDB for metabolite identification workflows?▼

HMDB querying requires precise identifier or structure/name concepts to retrieve accurate metabolite records. Without precise queries, candidate identification and spectral matching for biomarker discovery may return incomplete chemical or clinical context.

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