reactome-skill

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

Operating rules

• Use scripts/rest_request.py for all Reactome ContentService calls.
• Use base_url=https://reactome.org/ContentService.
• Single pathway or event lookups usually do not need max_items; list-style pathway membership calls are better with max_items=10.
• Send Accept: application/json in headers when requesting JSON.
• 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 these paths: data/query/<eventId>, data/pathways/low/entity/<identifier>, data/participants/<eventId>, and search endpoints.
• 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 Reactome patterns:
  • {"base_url":"https://reactome.org/ContentService","path":"data/query/R-HSA-199420","headers":{"Accept":"application/json"}}
  • {"base_url":"https://reactome.org/ContentService","path":"data/pathways/low/entity/P38398","params":{"species":"Homo sapiens"},"headers":{"Accept":"application/json"},"max_items":10}
  • {"base_url":"https://reactome.org/ContentService","path":"data/participants/R-HSA-199420","headers":{"Accept":"application/json"},"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://reactome.org/ContentService","path":"data/query/R-HSA-199420","headers":{"Accept":"application/json"}}' | 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.