Can I perform structure-based searches with this skill?

Yes, the skill provides guidance on using ChemQuery, SMILES, and InChI strings for structure and substructure searches within the HMDB ecosystem.

Can I use HMDB data for commercial purposes?

HMDB is freely available for academic and non-commercial research, but commercial use requires explicit permission from the authors at the University of Alberta.

What file formats are available for bulk HMDB data download?

Data is available in XML for comprehensive records, SDF for structures, FASTA for sequences, and CSV/TSV for tabular analysis.

Is there a public programmatic API for HMDB?

HMDB does not provide a public REST API; however, the skill outlines how researchers can request customized access or use R/Bioconductor packages like hmdbQuery.

What version of the HMDB database does this skill cover?

This skill covers HMDB version 5.0, which includes over 220,000 metabolite entries current as of 2025.

HMDB Scientific Database

Name: HMDB Scientific Database
Author: K-Dense-AI

byK-Dense-AI

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3,719

Data Science & ML

Accesses the Human Metabolome Database to retrieve chemical, clinical, and spectroscopic data for over 220,000 metabolites.

About

This skill provides comprehensive guidance for interacting with the Human Metabolome Database (HMDB) version 5.0, a crucial resource for metabolomics research, clinical chemistry, and biomarker discovery. It enables users to perform sophisticated searches by chemical structure, NMR/MS spectra, or disease associations, while offering detailed workflows for identifying metabolites and analyzing metabolic pathways within the human body. It is an essential tool for bioinformaticians and researchers looking to integrate high-quality metabolic data into their analysis pipelines.

Key Features

Search 220,000+ metabolites by name, ID, SMILES, or chemical structure
Guidance on bulk data downloads and programmatic API access for research
Retrieve experimental and predicted NMR and MS-MS spectroscopic data
Access detailed clinical data including biomarker associations and disease concentrations
Explore metabolic pathways, enzymatic reactions, and subcellular locations
3,719 GitHub stars

Use Cases

Discovering clinical biomarkers by correlating metabolite concentrations with specific diseases
Identifying unknown metabolites in untargeted metabolomics research using spectral matching
Integrating metabolic pathway analysis into bioinformatics and cheminformatics pipelines

About

Key Features

Search 220,000+ metabolites by name, ID, SMILES, or chemical structure
Guidance on bulk data downloads and programmatic API access for research
Retrieve experimental and predicted NMR and MS-MS spectroscopic data
Access detailed clinical data including biomarker associations and disease concentrations
Explore metabolic pathways, enzymatic reactions, and subcellular locations
3,719 GitHub stars

Use Cases

Discovering clinical biomarkers by correlating metabolite concentrations with specific diseases
Identifying unknown metabolites in untargeted metabolomics research using spectral matching
Integrating metabolic pathway analysis into bioinformatics and cheminformatics pipelines