Does this skill support spectral matching?

Yes, it facilitates workflows for matching experimental NMR, GC-MS, and LC-MS/MS spectra against the HMDB reference library for metabolite identification.

What is the HMDB Database skill used for?

It is used to research human metabolites, including their chemical properties, biological pathways, clinical biomarkers, and spectroscopic data for scientific research.

How many metabolites are included in the HMDB?

As of version 5.0, the database contains over 220,945 metabolite entries, covering both water-soluble and lipid-soluble compounds found in the human body.

Is an API required to use this skill?

The skill provides guidance on programmatic access using tools like the hmdbQuery R package or parsing bulk XML/CSV downloads, as HMDB does not offer a public REST API.

Can I search for metabolites using chemical structures?

Yes, the skill provides guidance on using SMILES, InChI strings, and substructure searches to find specific compounds within the database.

HMDB Scientific Database

Name: HMDB Scientific Database
Author: Zehong-Wang

byZehong-Wang

0•

Ciencia de Datos y ML

Accesses and queries the Human Metabolome Database (HMDB) for detailed metabolite information, chemical properties, and clinical biomarkers.

The HMDB Database skill provides Claude with specialized capabilities to interact with the Human Metabolome Database, a comprehensive resource of over 220,000 small molecule metabolites found in the human body. This tool is essential for researchers in metabolomics, clinical chemistry, and drug discovery, enabling them to search for metabolites by name, structure, or spectral data, retrieve clinical biomarker associations, and map biological pathways. By providing domain-specific guidance on data retrieval and analysis workflows, this skill streamlines the process of metabolite identification and biological interpretation within a Claude-powered environment.

Características Principales

010 GitHub stars

02Retrieve detailed chemical properties including SMILES, InChI, and molecular weight

03Search 220,000+ metabolites by name, HMDB ID, or chemical structure

04Access clinical data such as biomarker associations and concentration ranges

05Provide spectral matching data for NMR, GC-MS, and LC-MS identification

06Guide bulk data downloads and programmatic access via R or XML/CSV parsing

Casos de Uso

01Identifying unknown metabolites from experimental MS or NMR spectral data

02Researching disease-specific biomarkers and their metabolic pathway contexts

03Integrating HMDB chemical taxonomy and property data into bioinformatics pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos hmdb-database

For use in Claude.ai and ChatGPT