Can Claude perform spectral matching with this skill?

Yes, the skill allows for spectral searches including LC-MS, GC-MS, and NMR matching to help identify metabolites from experimental data.

What is the primary use of the HMDB Database skill?

It is used for metabolomics research, allowing AI agents to search for metabolites, analyze chemical structures, and identify biomarkers within the Human Metabolome Database.

Does this skill provide access to the latest HMDB data?

Yes, it is designed to interface with HMDB version 5.0, providing access to over 220,000 metabolite entries and 130+ data fields per compound.

Is this skill part of a larger framework?

Yes, it is part of the Kosmos AI Scientist project, which aims to create an autonomous AI for scientific discovery using Claude Code.

HMDB Scientific Database

Name: HMDB Scientific Database
Author: jimmc414

byjimmc414

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324

Data Science & ML

Provides comprehensive access to the Human Metabolome Database for metabolite identification, chemical analysis, and biomarker discovery.

About

The HMDB Database skill empowers Claude to act as a specialized scientific assistant by accessing over 220,000 human metabolite entries. It facilitates complex research workflows including structure-based searches, clinical biomarker identification, and spectral analysis for metabolomics. Integrated into the Kosmos AI Scientist framework, this skill enables automated discovery by retrieving chemical properties, metabolic pathways, and spectroscopic data directly from the Human Metabolome Database (v5.0), making it an essential tool for bioinformaticians and clinical researchers.

Key Features

Support for bulk dataset navigation and programmatic research workflows
Clinical and biological context including biomarker associations and pathways
324 GitHub stars
Advanced metabolite search by name, HMDB ID, SMILES, or InChI strings
Retrieval of detailed chemical properties, structures, and molecular formulas
Spectroscopic data access for LC-MS, GC-MS, and NMR spectral matching

Use Cases

Automating metabolite identification in untargeted metabolomics research
Cross-referencing experimental chemical data with known human biomarkers
Mapping metabolites to biological pathways for mechanistic discovery

About

Key Features

Support for bulk dataset navigation and programmatic research workflows
Clinical and biological context including biomarker associations and pathways
324 GitHub stars
Advanced metabolite search by name, HMDB ID, SMILES, or InChI strings
Retrieval of detailed chemical properties, structures, and molecular formulas
Spectroscopic data access for LC-MS, GC-MS, and NMR spectral matching

Use Cases

Automating metabolite identification in untargeted metabolomics research
Cross-referencing experimental chemical data with known human biomarkers
Mapping metabolites to biological pathways for mechanistic discovery