metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
npx skills add LeonChaoX/qinyan-academic-skills --skill metabolomics-workbench-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 **Exam
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Querying Metabolite Structures and Data
- 2. Accessing Study Metadata and Experimental Results
- 3. Standardizing Metabolite Nomenclature with RefMet
- 4. Performing Mass Spectrometry Searches
- 5. Filtering Studies by Analytical and Biological Parameters
- 6. Accessing Gene and Protein Information
- Common Workflows
- Workflow 1: Finding Studies for a Specific Metabolite
- Workflow 2: Identifying Compounds from MS Data
- Workflow 3: Exploring Disease-Specific Metabolomics
- Output Formats
What does the metabolomics-workbench-database skill do?
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill metabolomics-workbench-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.