Can I use this for commercial research?

While the skill is free to use, the HMDB database itself is free for academic use; commercial organizations must contact the HMDB team for specific licensing and API access.

Can I search for metabolites by chemical structure?

Yes, the skill provides protocols for structure-based searches using ChemQuery, SMILES, or InChI strings to identify specific metabolites within the database.

Does this skill provide clinical concentration data?

Yes, it can retrieve normal and abnormal concentration ranges for metabolites across various biological specimens like urine, serum, CSF, and saliva.

How up-to-date is the information provided?

The skill is optimized for HMDB version 5.0, which includes over 220,000 metabolite entries and is the current standard for human metabolome data as of 2025.

What is the HMDB Database skill?

It is a specialized Claude Code skill that enables the AI to access and interpret information from the Human Metabolome Database for scientific, clinical, and metabolomic research.

HMDB Scientific Database

Name: HMDB Scientific Database
Author: BbgnsurfTech

byBbgnsurfTech

•

数据科学与机器学习

Accesses the Human Metabolome Database (HMDB) to retrieve metabolite data, chemical properties, and biomarker information for scientific research.

The HMDB Database skill provides Claude with the specialized ability to navigate and extract data from the Human Metabolome Database, a comprehensive resource containing over 220,000 small molecule metabolites found in the human body. It enables researchers, clinicians, and data scientists to search for metabolites by name, ID, or structure, providing deep insights into chemical taxonomy, biological pathways, and clinical biomarker associations. This tool is indispensable for metabolomics workflows, clinical chemistry analysis, and identifying unknown compounds within human biological specimens.

主要功能

01Search 220,000+ metabolite entries by name, identifier, or chemical structure.

02Reference experimental and predicted NMR/MS spectra for metabolite identification.

03Map metabolites to specific metabolic pathways and associated enzymes.

04Retrieve detailed chemical properties including SMILES, InChI, and molecular weight.

05Access clinical biomarker data and normal/abnormal concentration ranges in biofluids.

063 GitHub stars

使用场景

01Investigating disease-related biomarkers and their concentration levels for clinical studies.

02Identifying unknown metabolites in untargeted metabolomics research using spectral matching.

03Mapping small molecule data to SMPDB pathways to understand biological mechanisms.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection hmdb-database

For use in Claude.ai and ChatGPT

Download Skill