pubchem-pug-skill

Imported from openai/plugins (plugins/life-science-research/skills/pubchem-pug-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill pubchem-pug-skill. Copyright stays with the author.

Operating rules

• Use scripts/rest_request.py for all PubChem PUG calls.
• Use base_url=https://pubchem.ncbi.nlm.nih.gov/rest/pug.
• Property and description endpoints usually return a single focused record; assay or broader list endpoints are better with max_items=10.
• Re-run requests in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Prefer property, description, assay summary, and substance paths instead of broad record dumps.
• If the user needs the full payload, set save_raw=true and report the saved file path.

Input

• Read one JSON object from stdin.
• Required fields: base_url, path
• Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common PubChem patterns:
  • {"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/name/aspirin/property/MolecularFormula,MolecularWeight/JSON","record_path":"PropertyTable.Properties"}
  • {"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/cid/2244/description/JSON","record_path":"InformationList.Information","max_items":10}
  • {"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"assay/aid/1706/summary/JSON","record_path":"AssaySummaries","max_items":10}

Output

• Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://pubchem.ncbi.nlm.nih.gov/rest/pug","path":"compound/name/aspirin/property/MolecularFormula,MolecularWeight/JSON","record_path":"PropertyTable.Properties"}' | python scripts/rest_request.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.