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pubchem-pug-skill

Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--pubchem-pug-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/pubchem-pug-skill/SKILL.md -o .claude/skills/pubchem-pug-skill.md

Drops the SKILL.md into .claude/skills/pubchem-pug-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

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.