metabolomics-workbench-database
Query Metabolomics Workbench Database
Also available from: davila7
Search and retrieve metabolomics data from the NIH Metabolomics Workbench database containing 4,200+ studies. Access metabolite structures, study metadata, RefMet nomenclature, and perform mass spectrometry searches.
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Using "metabolomics-workbench-database". Find all studies containing tyrosine
Expected outcome:
- Found 47 studies containing tyrosine:
- ST000001 - Comprehensive metabolomics analysis of amino acid metabolism
- ST000015 - Tyrosine metabolic pathways in liver tissue
- ST000042 - Serum amino acid profiling in metabolic disorders
- Study summary: The Metabolomics Workbench contains 47 studies measuring tyrosine across various tissues, species, and disease states.
Using "metabolomics-workbench-database". Search for compounds with m/z 180.06 using M+H adduct
Expected outcome:
- Top matches for m/z 180.06 (M+H, 0.5 Da tolerance):
- Registry 11: Glucose (C6H12O6) - exact mass 179.058
- Registry 156: Fructose (C6H12O6) - exact mass 179.058
- Registry 203: Mannose (C6H12O6) - exact mass 179.058
- Note: These monosaccharides share the same molecular formula
Security Audit
SafeAll 344 static findings are FALSE POSITIVES. The analyzer misidentified markdown documentation code blocks as shell commands, mass spectrometry ion adduct notation (M+H, M-H) as weak cryptographic algorithms, and legitimate database API calls as suspicious network activity. This is a documentation-only skill for the NIH Metabolomics Workbench - a legitimate scientific research database. No executable code exists.
Risk Factors
🌐 Network access (2)
⚙️ External commands (2)
📁 Filesystem access (1)
Quality Score
What You Can Build
Find studies for a metabolite
Search all metabolomics studies containing measurements of a specific metabolite like glucose or citrate.
Identify compounds from MS data
Input m/z values from mass spectrometry to identify potential metabolite candidates matching your data.
Filter studies by disease
Find metabolomics studies for specific diseases like diabetes or cancer using specific analytical platforms.
Try These Prompts
Find all studies in the Metabolomics Workbench that contain measurements of [metabolite_name]. Return study IDs and brief descriptions.
Search the Metabolomics Workbench for compounds matching m/z [value] with [M+H] adduct and 0.5 Da tolerance. List the top matches.
Use RefMet to standardize the metabolite name [common_name]. Return the standardized name and classification hierarchy.
Find human blood metabolomics studies on [disease_name] using [LCMS or GCMS or NMR] analytical method.
Best Practices
- Use RefMet to standardize metabolite names before searching studies for consistent results
- Set appropriate mass tolerance based on your instrument resolution (0.5 Da for low-res, 0.01 Da for high-res MS)
- Cache Ref making many queries toMet database locally when reduce API calls
Avoid
- Searching for metabolites without using RefMet standardization may miss relevant studies
- Using excessive mass tolerance returns too many false positive matches
- Making rapid sequential requests without delays may trigger rate limiting