hmdb-database

HMDB Database - Human Metabolome Database Query Tool

Skill Overview

The HMDB Database skill gives you quick access to the Human Metabolome Database (HMDB), allowing you to query detailed information on over 220,000 human metabolites, including chemical properties, biomarker data, NMR/MS spectra, and metabolic pathways.

Use Cases

1. Metabolomics Research

When conducting metabolomics experiments and needing to identify unknown metabolites or look up detailed information on known metabolites, HMDB can quickly provide compound structures, molecular weights, spectral data, and biological functions to accelerate your research.

2. Metabolite Identification and Validation

After mass spectrometry (MS) or nuclear magnetic resonance (NMR) analysis, use HMDB's spectral matching features to compare experimental data with reference spectra and accurately identify metabolites. Multiple search methods are supported (name, ID, structure, SMILES, InChI).

3. Biomarker Discovery and Clinical Research

Query disease-related metabolites and their concentration ranges in normal and pathological states to explore potential biomarkers, and obtain clinically relevant concentration data and toxicology information.

Core Features

1. Multi-dimensional Metabolite Search

Supports searches by name, HMDB ID, structural formula, and molecular weight range. Provides LC-MS, GC-MS, and NMR spectral matching capabilities, and allows filtering metabolites by biological sample type (urine, serum, cerebrospinal fluid, etc.).

2. Comprehensive Metabolite Information

Provides detailed information across 130+ data fields, including chemical properties (structure, molecular formula, SMILES), biological context (metabolic pathways, enzymes, localization), clinical relevance (normal concentrations, disease associations, biomarkers), and analytical data (NMR/MS spectra, retention times).

3. Bulk Data Download and Local Analysis

Supports export in multiple formats such as XML, SDF, CSV/TSV, and FASTA, facilitating the construction of local databases or integration into data analysis pipelines. Suitable for large-scale data processing and further development.

Frequently Asked Questions

Is the HMDB Database free?

HMDB is freely available for academic and non-commercial research. Commercial use requires explicit permission from the authors, and users must acknowledge the data source (HMDB) and the original publications. When downloading large amounts of data, please cite the relevant HMDB publications in any resulting papers.

How do I search for metabolites in HMDB?

You can search in various ways: enter a metabolite name, synonym, or HMDB ID (e.g., HMDB0000001) for text searches; use ChemQuery for structure or substructure searches; upload experimental spectra for LC-MS, GC-MS, or NMR matching; or apply advanced filters by disease association, pathway, or sample type.

Can HMDB be used for commercial purposes?

Commercial use requires you to contact the HMDB team (samackay@ualberta.ca) to obtain permission. Academic research teams needing programmatic access can contact eponine@ualberta.ca or samackay@ualberta.ca. R users can query HMDB using the hmdbQuery package from Bioconductor.