pubchem-pug-skill — Codex skill: what it does, how to install
Runs targeted PubChem PUG REST requests to extract molecular properties, compound descriptions, and biological assay summaries.
npx skills add openai/plugins --skill pubchem-pug-skill -a codexWhat pubchem-pug-skill 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.
What it helps with
- 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 for the agent
- 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
How to install pubchem-pug-skill
1Skills CLI (Vercel)
npx skills add openai/plugins --skill pubchem-pug-skill -a codex2Manually: put the files in place
.agents/skills/pubchem-pug-skill/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add openai/plugins --skill pubchem-pug-skill -a claude-code2Manually: put the files in place
~/.claude/skills/pubchem-pug-skill/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/pubchem-pug-skill/
Manually: put the files in place
.cursor/skills/pubchem-pug-skill/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install openai/plugins pubchem-pug-skill2Manually: put the files in place
.github/skills/pubchem-pug-skill/SKILL.mdPlatform CLI
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/pubchem-pug-skillManually: put the files in place
.devin/skills/pubchem-pug-skill/SKILL.mdThe legacy .windsurf/skills/ path still works
Claude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: Codex skills: how to install, where they live, how to call them
Questions about pubchem-pug-skill
How do I install pubchem-pug-skill in Codex?
Run npx skills add openai/plugins --skill pubchem-pug-skill in your terminal. You can also specify the target agent by executing npx skills add openai/plugins --skill pubchem-pug-skill -a codex.
What does pubchem-pug-skill do?
It submits compact REST queries to the PubChem PUG interface, returning focused summaries of compound data, substance records, and assay metrics.
How does the skill execute PubChem requests?
It feeds a JSON payload via standard input into scripts/rest_request.py, requiring Python in your runtime environment.
