Is there a public REST API for HMDB?

HMDB does not provide a standard public REST API. This skill provides instructions on how to request programmatic access or use the hmdbQuery R/Bioconductor package.

Can I download HMDB data for local analysis?

Yes, the skill provides information on how to retrieve bulk datasets in XML, SDF, and CSV formats for integration into local data analysis pipelines.

Does this skill provide spectral data for compound identification?

Yes, it assists in accessing reference NMR, MS, and MS-MS spectra to help identify metabolites found in experimental samples.

Can I search the HMDB by chemical structure using this skill?

Yes, this skill supports guidance for searching via chemical representations like SMILES or InChI strings to find specific metabolites within the database.

Is HMDB data free for commercial use?

HMDB is free for academic and non-commercial research; however, commercial organizations require explicit permission from the development team.

HMDB Database Assistant

Name: HMDB Database Assistant
Author: Microck

byMicrock

•

データサイエンスとML

Accesses the Human Metabolome Database to retrieve metabolite properties, clinical biomarker data, and spectral information for metabolomics research.

概要

This skill empowers Claude to interact with the Human Metabolome Database (HMDB), a massive repository containing over 220,000 human metabolites. It streamlines complex research workflows by enabling searches for compounds via name, ID, structure, or spectral data, while providing deep biological context including pathway associations and clinical biomarker data. Whether performing untargeted metabolomics identification or investigating disease-specific chemical concentrations, this tool serves as a bridge between AI-assisted coding and high-fidelity biochemical data.

主な機能

81 GitHub stars
Retrieval of biological context including metabolic pathways and enzyme associations
Guidance on programmatic data access via XML, SDF, and R/Bioconductor packages
Access to clinical data including disease associations and normal concentration ranges
Integration with spectral data (NMR, MS, MS-MS) for compound identification
Comprehensive metabolite search by name, HMDB ID, SMILES, or InChI strings

ユースケース

Mapping metabolite lists to metabolic pathways for biological interpretation and enrichment analysis
Identifying unknown metabolites in untargeted metabolomics studies using spectral matching
Researching clinical biomarkers and their associated concentration ranges in human biological fluids

概要

主な機能

81 GitHub stars
Retrieval of biological context including metabolic pathways and enzyme associations
Guidance on programmatic data access via XML, SDF, and R/Bioconductor packages
Access to clinical data including disease associations and normal concentration ranges
Integration with spectral data (NMR, MS, MS-MS) for compound identification
Comprehensive metabolite search by name, HMDB ID, SMILES, or InChI strings

ユースケース

Mapping metabolite lists to metabolic pathways for biological interpretation and enrichment analysis
Identifying unknown metabolites in untargeted metabolomics studies using spectral matching
Researching clinical biomarkers and their associated concentration ranges in human biological fluids