{"id":12153,"plugin_id":"Plugin_054ff933a434819187c4f95db80afc7f","kind":"skill","collection_source":null,"comparison_source":null,"observed_at":"2026-09-30T23:00:59.661Z","digest":"c139ae607324f7ff6a860efd3a87ed8b3ded85b668773b089d8937b59f9b581b","against":null,"payload":{"name":"biostudies-arrayexpress-skill","description":"Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries","included_files":[{"relative_path":"scripts/rest_request.py","size_in_bytes":1097}],"skill_md_contents":"---\nname: biostudies-arrayexpress-skill\ndescription: Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries\n---\n\n## Source presentation\n<!-- source-presentation-contract:v2 -->\n- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.\n- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.\n- Use the `biostudies-arrayexpress-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/rest_request.py` for all BioStudies and ArrayExpress calls.\n- Use `base_url=https://www.ebi.ac.uk/biostudies/api/v1`.\n- Search pages are better with `pageSize=10` and `max_items=10`; accession lookups usually do not need `max_items`.\n- Re-run requests in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Prefer these paths: `search`, `ArrayExpress/search`, `studies/<accession>`, and `studies/<accession>/info`.\n- If the user needs the full payload, set `save_raw=true` and report the saved file path instead of pasting large study records into chat.\n\n## Input\n- Read one JSON object from stdin.\n- Required fields: `base_url`, `path`\n- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common BioStudies patterns:\n  - `{\"base_url\":\"https://www.ebi.ac.uk/biostudies/api/v1\",\"path\":\"search\",\"params\":{\"query\":\"rna\",\"page\":1,\"pageSize\":10},\"record_path\":\"hits\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/biostudies/api/v1\",\"path\":\"ArrayExpress/search\",\"params\":{\"query\":\"single cell\",\"page\":1,\"pageSize\":10},\"record_path\":\"hits\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/biostudies/api/v1\",\"path\":\"studies/E-MTAB-6701\"}`\n\n## Output\n- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"base_url\":\"https://www.ebi.ac.uk/biostudies/api/v1\",\"path\":\"search\",\"params\":{\"query\":\"rna\",\"page\":1,\"pageSize\":10},\"record_path\":\"hits\",\"max_items\":10}' | python scripts/rest_request.py\n```\n"},"changes":[],"summary":"First saved snapshot. No earlier version is available for comparison.","summary_kind":"deterministic","summary_metadata":{}}