metabolomics-workbench-database SKILL.md skillA
metabolomics-workbench-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/metabolomics-workbench-database@git:20260522.6a6fd41Pins git:20260522.6a6fd41 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/proteomics-protein-engineering/metabolomics-workbench-database/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260522.6a6fd41, committed May 22, 2026
- First version recorded
- Feb 18, 2026
- Size
- 21,307 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Metabolomics Workbench Database — REST API Access
## Overview
The Metabolomics Workbench (MW) REST API at `https://www.metabolomicsworkbench.org/rest/` exposes 4,200+ metabolomics studies hosted at UCSD under NIH Common Fund sponsorship. URL pattern is `/{context}/{input_item}/{input_value}/{output_item}/{format}`. Contexts include `compound`, `refmet`, `moverz`, `study`, `analysis`, `metabolite`, `gene`, `protein`. Notable quirks discovered live:
- `compound/name/{x}` is **rejected** — `name` is not an allowed input_item. Use `pubchem_cid`, `kegg_id`, `inchi_key`, `hmdb_id`, `regno`, `lm_id`, `formula`, `smiles`, or `abbrev`. For free-text input, go through `refmet/match/{x}` first.
- `refmet/name/{x}/all` requires the **exact** RefMet name (e.g. `Glucose`, not `D-glucose`); use `refmet/match/{x}` for fuzzy normalisation first.
- `moverz/{REFMET|LIPIDS|MB}/{mz}/{ion}/{tol}/txt` returns **TSV text** (no JSON variant).
- The `metstat/filter/...` endpoint shown in older examples returns `[]` — replace with `study/{context}/{value}/summary` (or `/metabolites`) + client-side filtering.
No authentication required.
## When to Use
…Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/metabolomics-workbench-database@sha256:e79051a7ff58ea46The line at the top of this page pins the label git:20260522.6a6fd41, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_jb4aqrhsgeoqpb4f)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and May 22, 2026, about one every 46 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260522.6a6fd41 latest | 2026-05-22 | 6a6fd41 | 21,307 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 22,384 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 22,465 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (21307 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jb4aqrhsgeoqpb4f GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/metabolomics-workbench-database GET https://markdownregistry.com/api/v1/blob/e79051a7ff58ea46fafba8ff9e9f1e95ab666cd42cbd4f13f20a71ef246d732f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.