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Improve database description for more reliable skill calling

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Timothy Kassis
2025-10-20 16:02:48 -07:00
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scientific-databases/metabolomics-workbench-database/SKILL.md
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name: metabolomics-workbench-database
description: Toolkit for accessing and querying the Metabolomics Workbench, an NIH-sponsored repository containing 4,200+ metabolomics studies with standardized nomenclature (RefMet), study metadata, experimental results, and comprehensive metabolite databases. Use this skill when working with metabolomics data, querying metabolite structures, accessing study results, standardizing metabolite names, performing mass spectrometry searches, or retrieving gene/protein associations with metabolites.
description: Comprehensive toolkit for accessing and analyzing metabolomics data through the Metabolomics Workbench REST API. This NIH-sponsored repository contains 4,200+ metabolomics studies with standardized RefMet nomenclature, experimental datasets, metabolite structures, and gene/protein associations. Use this skill for: querying metabolite structures and downloading molecular data (MOL files, PNG images), accessing study metadata and experimental results from GC-MS/LC-MS/NMR platforms, standardizing metabolite names using RefMet classification system, performing mass spectrometry searches by m/z values with ion adducts, filtering studies by analytical methods (LCMS/GCMS/NMR), ionization polarity (positive/negative), chromatography types (HILIC/RP/GC), species, sample sources, and diseases, retrieving gene and protein information related to metabolic pathways, cross-referencing metabolite identifiers across databases (PubChem, KEGG, HMDB), identifying compounds from MS data using exact mass calculations, exploring disease-specific metabolomics studies, accessing untargeted metabolomics datasets, and retrieving complete experimental data in JSON or TXT formats. Essential for metabolomics research, biomarker discovery, metabolic pathway analysis, and mass spectrometry data interpretation.
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# Metabolomics Workbench Database