Can I use this skill to identify unknown metabolites?

Yes, the skill supports mass-to-charge (m/z) searches with various ion adducts and mass tolerances to help identify potential compounds.

What is the primary source of data for this skill?

This skill accesses the NIH Common Fund's Metabolomics Workbench repository hosted at UCSD, containing over 4,200 processed metabolomics studies.

What output formats are supported for the data?

The skill primarily retrieves data in JSON format for programmatic use, but also supports human-readable tab-delimited text (TXT).

Does it provide access to gene and protein information?

Yes, it can retrieve gene and protein data associated with specific metabolic pathways and metabolite metabolism.

How does this skill help with inconsistent metabolite naming?

It utilizes the RefMet database to map common names to a standardized nomenclature and hierarchical chemical classification.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: K-Dense-AI

byK-Dense-AI

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2,188

Data Science & ML

Accesses the NIH Metabolomics Workbench to query over 4,200 studies, standardize metabolite nomenclature, and perform mass spectrometry searches.

About

The Metabolomics Workbench Database skill enables seamless programmatic access to the NIH Common Fund's primary repository for metabolomics research. It allows researchers and developers to retrieve detailed study metadata, standardized compound information via RefMet, and experimental results from thousands of public studies. Whether you are performing biomarker discovery, standardizing chemical nomenclature, or identifying compounds from mass spectrometry (m/z) data, this skill provides the necessary endpoints and workflows to integrate scientific data directly into your Claude-assisted research environment.

Key Features

Precursor ion search by m/z value with customizable adducts and tolerances
2,188 GitHub stars
Standardized metabolite nomenclature and classification using RefMet
REST API access to 4,200+ metabolomics studies and experimental datasets
Retrieval of molecular structures (MOL, PNG) and database cross-references
Gene and protein association mapping for metabolic pathways

Use Cases

Standardizing diverse metabolite lists using RefMet hierarchical classification
Automating the retrieval of experimental data for specific diseases or analytical methods
Identifying unknown compounds by searching m/z values against the Metabolomics Workbench database

About

Key Features

Precursor ion search by m/z value with customizable adducts and tolerances
2,188 GitHub stars
Standardized metabolite nomenclature and classification using RefMet
REST API access to 4,200+ metabolomics studies and experimental datasets
Retrieval of molecular structures (MOL, PNG) and database cross-references
Gene and protein association mapping for metabolic pathways

Use Cases

Standardizing diverse metabolite lists using RefMet hierarchical classification
Automating the retrieval of experimental data for specific diseases or analytical methods
Identifying unknown compounds by searching m/z values against the Metabolomics Workbench database