Metabolomics Workbench (Claude Skill)

Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.

   
Type Claude Skill
Supplier jaechang-hits (community OSS, CC BY 4.0)
Availability GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing Free / OSS (CC-BY-4.0)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

  • Claude Code — clone and load as a plugin: 
    git clone https://github.com/jaechang-hits/SciAgent-Skills

    Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.

  • Manual / other agents — point the agent at the skill file directly: 
    cp -r SciAgent-Skills/skills/proteomics-protein-engineering/metabolomics-workbench-database ~/.claude/skills/

    The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations. Quirks: compound input_item rejects name (use pubchem_cid/kegg_id/inchi_key/etc.); free-text → compound is a two-step refmet/match→refmet/name flow; moverz endpoint returns TSV text, not JSON. Use hmdb-database for local XML; pubchem-compound-search for general compound lookup.

Primary use cases: Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: CC-BY-4.0. The skill directory upstream is skills/proteomics-protein-engineering/metabolomics-workbench-database.

Sources

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