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SKILL.md
Metabolomics Workbench Database
Overview
The Metabolomics Workbench is a comprehensive NIH Common Fund-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data. It provides programmatic access to over 4,200 processed studies (3,790+ publicly available), standardized metabolite nomenclature through RefMet, and powerful search capabilities across multiple analytical platforms (GC-MS, LC-MS, NMR).
When to Use This Skill
This skill should be used when querying metabolite structures, accessing study data, standardizing nomenclature, performing mass spectrometry searches, or retrieving gene/protein-metabolite associations through the Metabolomics Workbench REST API.
Core Capabilities
1. Querying Metabolite Structures and Data
Access comprehensive metabolite information including structures, identifiers, and cross-references to external databases.
Key operations:
Retrieve compound data by various identifiers (PubChem CID, InChI Key, KEGG ID, HMDB ID, etc.)
Download molecular structures as MOL files or PNG images
Access standardized compound classifications
Cross-reference between different metabolite databases
Example queries:
import requests
# Get compound information by PubChem CID
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
# Download molecular structure as PNG
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png')
# Get compound name by registry number
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json')
2. Accessing Study Metadata and Experimental Results
Query metabolomics studies by various criteria and retrieve complete experimental datasets.
Key operations:
Search studies by metabolite, institute, investigator, or title
Access study summaries, experimental factors, and analysis details
Retrieve complete experimental data in various formats
Download mwTab format files for complete study information
Query untargeted metabolomics data
Example queries:
# List all available public studies
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json')
# Get study summary
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json')
# Retrieve experimental data
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json')
# Find studies containing a specific metabolite
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json')
3. Standardizing Metabolite Nomenclature with RefMet
Use the RefMet database to standardize metabolite names and access systematic classification across four structural resolution levels.
Key operations:
Match common metabolite names to standardized RefMet names
Query by chemical formula, exact mass, or InChI Key
Access hierarchical classification (super class, main class, sub class)
Retrieve all RefMet entries or filter by classification
Example queries:
# Standardize a metabolite name
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json')
# Query by molecular formula
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all/json')
# Get all metabolites in a specific class
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json')
# Retrieve complete RefMet database
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/all/json')
4. Performing Mass Spectrometry Searches
Search for compounds by mass-to-charge ratio (m/z) with specified ion adducts and tolerance levels.
Key operations:
Search precursor ion masses across multiple databases (Metabolomics Workbench, LIPIDS, RefMet)
Specify ion adduct types (M+H, M-H, M+Na, M+NH4, M+2H, etc.)
Calculate exact masses for known metabolites with specific adducts
Set mass tolerance for flexible matching
Example queries:
# Search by m/z value with M+H adduct
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json')
# Calculate exact mass for a metabolite with specific adduct
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json')
# Search across RefMet database
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json')
5. Filtering Studies by Analytical and Biological Parameters
Use the MetStat context to find studies matching specific experimental conditions.
Key operations:
Filter by analytical method (LCMS, GCMS, NMR)
Specify ionization polarity (POSITIVE, NEGATIVE)
Filter by chromatography type (HILIC, RP, GC)
Target specific species, sample sources, or diseases
Combine multiple filters using semicolon-delimited format
Example queries:
# Find human blood studies on diabetes using LC-MS
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json')
# Find all human blood studies containing tyrosine
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json')
# Filter by analytical method only
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json')
6. Accessing Gene and Protein Information
Retrieve gene and protein data associated with metabolic pathways and metabolite metabolism.
Key operations:
Query genes by symbol, name, or ID
Access protein sequences and annotations
Cross-reference between gene IDs, RefSeq IDs, and UniProt IDs
Retrieve gene-metabolite associations
Example queries:
# Get gene information by symbol
response = requests.get('https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json')
# Retrieve protein data by UniProt ID
response = requests.get('https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json')
Common Workflows
Workflow 1: Finding Studies for a Specific Metabolite
To find all studies containing measurements of a specific metabolite:
First standardize the metabolite name using RefMet:
JSON (default): Machine-readable format, ideal for programmatic access
TXT: Human-readable tab-delimited text format
Specify format by appending /json or /txt to API URLs. When format is omitted, JSON is returned by default.
Best Practices
Use RefMet for standardization: Always standardize metabolite names through RefMet before searching studies to ensure consistent nomenclature
Specify appropriate adducts: When performing m/z searches, use the correct ion adduct type for your analytical method (e.g., M+H for positive mode ESI)
Set reasonable tolerances: Use appropriate mass tolerance values (typically 0.5 Da for low-resolution, 0.01 Da for high-resolution MS)
Cache reference data: Consider caching frequently used reference data (RefMet database, compound information) to minimize API calls
Handle pagination: For large result sets, be prepared to handle multiple data structures in responses
Validate identifiers: Cross-reference metabolite identifiers across multiple databases when possible to ensure correct compound identification
Resources
references/
Detailed API reference documentation is available in references/api_reference.md, including:
Complete REST API endpoint specifications
All available contexts (compound, study, refmet, metstat, gene, protein, moverz)
Input/output parameter details
Ion adduct types for mass spectrometry
Additional query examples
Load this reference file when detailed API specifications are needed or when working with less common endpoints.
