ncbi-pmc-skill

Imported from SciMiner/sciminer-skills (pharma-intelligence/skills/ncbi-pmc-skill/SKILL.md). Install upstream with npx skills add SciMiner/sciminer-skills --skill ncbi-pmc-skill. Copyright stays with the author.

Operating rules

• Use scripts/ncbi_pmc.py for all PMC Open Access calls in this package.
• This skill is intentionally narrow: it currently covers the PMC Open Access service rather than the full PMC API surface.
• Pass endpoint-specific query parameters under params, typically id for a PMCID or DOI-style lookup supported by the OA service.
• 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 output by default.
• Return raw XML only if the user explicitly asks for machine-readable output.
• Prefer targeted endpoint calls instead of broad unfiltered dumps.
• If the user needs the full raw response, set save_raw=true and report the saved file path.

Input

• Read one JSON object from stdin.
• Optional fields: params, record_path, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common PMC Open Access patterns:
  • {"params":{"id":"PMC3257301"},"max_items":10}
  • {"params":{"id":"10.1093/nar/gkr1184"},"max_items":10}

Output

• Success returns ok, source, and a compact summary.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"params":{"id":"PMC3257301"},"max_items":10}' | python scripts/ncbi_pmc.py

References

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