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version: "1.0.1" name: pubchem-pug-skill description: Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries
Operating rules
- Use
scripts/rest_request.pyfor 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=trueand 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 compactrecordsor a compactsummary. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
bash
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.