pride-skill

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

Operating rules

• Use scripts/rest_request.py for all PRIDE Archive calls.
• Use base_url=https://www.ebi.ac.uk/pride/ws/archive/v2.
• Start with projects for discovery and keep page sizes modest.
• Prefer project-level metadata lookups over broad archive dumps.
• Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return raw JSON only if the user explicitly asks for machine-readable output.
• Prefer these paths: projects and projects/<PXD accession>.

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 PRIDE patterns:
  • {"base_url":"https://www.ebi.ac.uk/pride/ws/archive/v2","path":"projects","params":{"keyword":"proteomics","pageSize":10},"max_items":10}
  • {"base_url":"https://www.ebi.ac.uk/pride/ws/archive/v2","path":"projects/PXD001357"}

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://www.ebi.ac.uk/pride/ws/archive/v2","path":"projects","params":{"keyword":"proteomics","pageSize":10},"max_items":10}' | 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.