Does this skill provide a direct REST API for HMDB?

No, HMDB does not offer a public REST API. This skill provides guidance on using the web interface, R/Bioconductor packages, or parsing bulk XML/SDF downloads for programmatic access.

Is the data provided by this skill up to date?

The skill is optimized for HMDB version 5.0, the current standard containing the most recent metabolite entries and clinical associations.

What type of data does the HMDB skill provide?

It provides comprehensive data on human metabolites, including chemical structures, clinical biomarkers, NMR/MS spectra, and metabolic pathways.

Can I use this skill for commercial research?

While the database is free for academic use, commercial applications require explicit permission from the HMDB development team at the University of Alberta.

HMDB Scientific Database

Name: HMDB Scientific Database
Author: sanand0

bysanand0

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Data Science & ML

Accesses the Human Metabolome Database to retrieve chemical properties, clinical biomarkers, and spectral data for metabolomics research.

The HMDB Scientific Database skill integrates Claude with the Human Metabolome Database (HMDB), providing instant access to over 220,000 metabolite entries. It enables researchers to perform complex queries regarding chemical structures, biological pathways, and clinical biomarkers directly within their workflow. Whether you're identifying unknown metabolites from MS/NMR spectra or researching disease-specific concentration ranges, this skill streamlines the retrieval of high-quality scientific data, supporting both manual lookups and programmatic data analysis through XML and SDF formats.

Key Features

01Search 220,000+ metabolites by name, ID, or chemical structure

02Retrieve detailed chemical properties including SMILES, InChI, and formulas

03Consult biological pathway information and protein-enzyme associations

04Guidance for bulk data processing using XML, SDF, and R/Bioconductor

05Access clinical data on disease-metabolite associations and concentration ranges

063 GitHub stars

Use Cases

01Mapping metabolites to biological pathways for biomarker discovery

02Identifying unknown metabolites during untargeted metabolomics research

03Automating the collection of reference chemical data for scientific publications

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sanand0/scientific-research hmdb-database

For use in Claude.ai and ChatGPT

Download Skill