hmdb-database

Name: hmdb-database
Availability: InStock
Author: rubensliv

Retrieve HMDB metabolite properties, spectra, and disease associations from XML/CSV datasets.

15|2|Updated Dec 17, 2025

Search Tags:#metabolomics #pathways #cross-database #hmdb #spectra #biomarkers #metabolite-search

Ready to run

npx skills add https://github.com/rubensliv/k-dense-ai --skill hmdb-database-rubensliv

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/hmdb-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill hmdb-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

HMDB provides rich, structured data on human metabolites. This Skill enables researchers to quickly locate HMDB entries and retrieve chemical properties, spectra, biomarker data, pathways, and cross-references for metabolomics workups.

Core Features & Use Cases

Metabolite searches by name, HMDB ID, SMILES, or InChI, returning relationships to pathways, diseases, and enzymes.
Retrieve chemical data (formula, weight, SMILES, InChI, InChIKey) and spectroscopic data (NMR, MS) for identification and reporting.
Cross-reference with external databases (KEGG, PubChem, SMPDB, ChEBI) to enable integrated analyses and literature linking.

Quick Start

Query HMDB for a metabolite by name, HMDB ID, SMILES, or InChI to retrieve its properties, pathways, and references.

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 a metabolite using a chemical identifier?▼

You can search HMDB for a metabolite using its name, HMDB ID, SMILES, or InChI string. This retrieves chemical properties, pathways, disease associations, and spectroscopic data to support metabolomics workflows.

What metabolite data is available from HMDB for biomarker discovery?▼

HMDB metabolite data for biomarker discovery includes chemical properties, NMR and MS spectra, disease associations, and pathway relationships. This supports metabolite identification and pathway analysis in research settings.

Can I cross-reference HMDB metabolite data with external databases like KEGG and PubChem?▼

Yes, HMDB data can be cross-referenced with external databases including KEGG, PubChem, SMPDB, and ChEBI. This enables integrated analyses and literature linking across multiple chemical biology platforms.

What's the best way to retrieve NMR and MS spectra for metabolite identification?▼

The best way to retrieve NMR and MS spectra for metabolite identification is to query HMDB by metabolite name or identifier. This returns spectroscopic data alongside chemical properties for accurate reporting.

Do I need downloaded HMDB XML or CSV datasets for programmatic metabolomics analysis?▼

Yes, programmatic use of HMDB data is enabled through downloaded XML and CSV datasets. These structured datasets support integrated analysis and cross-database connections for metabolomics workflows.