# pubchem-pug-skill

Runs targeted PubChem PUG REST requests to extract molecular properties, compound descriptions, and biological assay summaries.

- skill · `type=skill` · Codex, ChatGPT · 14 installs · ★ 7596
- Author: OpenAI · official OpenAI repository
- License: LicenseRef-Proprietary · policy=link-only · description only; the file stays with the author
- Source: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/pubchem-pug-skill/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/pubchem-pug-skill

## What it does

This skill queries the PubChem chemistry database without pulling heavy payload dumps into the conversation. It structures direct calls against `https://pubchem.ncbi.nlm.nih.gov/rest/pug` to retrieve chemical details such as molecular weight, formula, or compound descriptions by CID.

Requests execute via the bundled `scripts/rest_request.py` script through standard input. The tool formats script output as a concise markdown summary by default. Whenever you need the complete response body, passing `save_raw=true` writes the full content to the path designated by `raw_output_path`.

Running the helper script requires a functional Python setup. Because assay and catalog listings can grow quickly, the tool caps these queries using `max_items=10` to avoid bloating the agent context.

## Install

### Codex (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill pubchem-pug-skill -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/pubchem-pug-skill/SKILL.md` — For all projects use ~/.agents/skills/

### Claude Code

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill pubchem-pug-skill -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/pubchem-pug-skill/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/pubchem-pug-skill/

### Cursor

**Manually: put the files in place**
- File: `.cursor/skills/pubchem-pug-skill/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install openai/plugins pubchem-pug-skill
```

2. **Manually: put the files in place**
- File: `.github/skills/pubchem-pug-skill/SKILL.md`

### Gemini CLI

**Platform CLI**
```bash
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/pubchem-pug-skill
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/pubchem-pug-skill/SKILL.md` — The legacy .windsurf/skills/ path still works

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/pubchem-pug-skill/SKILL.md

## When to use it
- fetch molecular weights and formulas by compound name
- retrieve compound descriptions using a PubChem CID
- pull screening assay summaries by AID
- store raw REST response payloads directly to disk

## Example prompts
- Look up the molecular formula and weight for aspirin in PubChem
- Fetch the summary and description for compound CID 2244
- Get assay summary details for AID 1706 and save the raw JSON

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From the same set: [openai/plugins](https://affpapa.org/en/nevibecode/by/openai/plugins.md) — 422 cards

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