Can I perform structure-based searches with this skill?

Yes, the skill provides guidance on using ChemQuery, SMILES, and InChI strings to search for metabolites by their chemical structure within the HMDB ecosystem.

How does this help with metabolomics workflows?

It assists in metabolite identification, spectral matching, and pathway analysis by providing the correct procedures for querying HMDB's extensive biological and chemical datasets.

What is the HMDB Claude Code skill?

It is a specialized capability that provides Claude with structured knowledge and best practices for accessing the Human Metabolome Database (HMDB) for research and data analysis.

Is clinical data included in the database?

Yes, HMDB includes detailed clinical information such as normal/abnormal concentration ranges, disease associations, and biomarker data for thousands of metabolites.

Does this skill require a paid API key for HMDB?

HMDB is free for academic and non-commercial use. While the skill helps you navigate the database, programmatic API access requires contacting the HMDB development team directly.

HMDB Metabolomics Database

Name: HMDB Metabolomics Database
Author: Activer007

byActiver007

0•

データサイエンスとML

Provides comprehensive access to the Human Metabolome Database (HMDB) for metabolite identification, chemical analysis, and clinical research.

This skill integrates the vast resources of the Human Metabolome Database into the Claude Code environment, enabling researchers and developers to query over 220,000 metabolite entries. It facilitates complex workflows including structure-based searches via SMILES or InChI, spectral matching for MS and NMR data, and retrieval of clinical biomarker information. Whether you are performing untargeted metabolomics, studying metabolic pathways, or developing bioinformatics pipelines, this skill provides the necessary guidance and best practices for leveraging HMDB's chemical, biological, and clinical data effectively within your development workflow.

主な機能

01Access to 220,000+ metabolite entries with chemical and clinical data

020 GitHub stars

03Support for structure-based searches using SMILES and InChI strings

04Integration with biological pathways and clinical biomarker associations

05Spectral matching guidance for NMR, MS, and MS-MS data

06Bulk dataset download management in XML, SDF, and CSV formats

ユースケース

01Identifying metabolites from experimental MS or NMR spectra in untargeted metabolomics studies

02Mapping metabolic pathways and enzymatic reactions for biological data interpretation

03Discovering clinical biomarkers by correlating metabolite concentrations with specific diseases

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills hmdb-database

For use in Claude.ai and ChatGPT

Download Skill