metabolomics-workbench-database

metabolomics-workbench-database is a skill for Claude Code from jimmc414/Kosmos. It costs 53 tokens per session (2,329 once invoked), scanned A, original, no licence file.

A way to access the NIH Metabolomics Workbench, a database of studies measuring small molecules in biological samples. It supports searches for metabolites, chemical names, mass-to-charge values, nuclear-magnetic-resonance data, and study details.

In plain words
What is it for?
Use it to query metabolite records, search MS or NMR measurements, inspect study metadata, and investigate possible biomarkers.
Why use it?
It avoids manually browsing a large metabolomics database when looking for matching studies or compounds. It provides a programmatic route to data used in metabolomics and biomarker work.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the scientific-skills plugin — 119 skills shipped together

Good fit Use it to query metabolite records, search MS or NMR measurements, inspect study metadata, and investigate possible biomarkers.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimmc414/kosmos/metabolomics-workbench-database
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add jimmc414/Kosmos --skill metabolomics-workbench-database
Clone the repo
git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code.

Or install scientific-skills, the plugin that ships this one along with the rest of its 119 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for metabolomics-workbench-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimmc414/kosmos/metabolomics-workbench-database.svg)](https://agentmods.dev/skills/jimmc414/kosmos/metabolomics-workbench-database)
Your own site
<a href="https://agentmods.dev/skills/jimmc414/kosmos/metabolomics-workbench-database"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/metabolomics-workbench-database.svg" alt="Measured on agentmods" height="20"></a>
Per session 53 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,329 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00053 $0.02329
Opus 5 $0.00026 $0.01164
Sonnet 5 $0.00011 $0.00466
Haiku 4.5 $0.00005 $0.00233

Measured 4d ago against content hash 4ea74ad8c736, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

metabolomics-workbench-database scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
kosmos-claude-scientific-skills/scientific-skills/metabolomics-workbench-database/SKILL.md · 254 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 4d ago First seen · 254 lines · 53 tokens per session scan A 4ea74ad8c736

Subscribe to this mod's changes

metabolomics-workbench-database is a skill published in the GitHub repository jimmc414/Kosmos (579 stars, last pushed 5mo ago), with no licence file. It adds 53 tokens to every session and 2,329 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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