| name | reactome-event-summary |
| description | Use this skill to fetch a concise summary for a known Reactome event or pathway stable ID from the official Reactome Content Service. Do not use it for full pathway traversal, graph expansion, or unsupported Reactome endpoints. |
Purpose
Fetch a compact JSON summary for a known Reactome stable ID by calling the official Content Service data/query/<stable-id> endpoint.
When to use
- You already know the Reactome stable ID, such as
R-HSA-141409.
- You want a lightweight event or pathway summary with the display name, species, compartment, and summary text.
When not to use
- You need pathway membership expansion or contained-event traversal.
- You need bulk downloading or unsupported Reactome endpoints.
Inputs
- Reactome stable ID
- Optional output path
Outputs
- A JSON summary derived from
https://reactome.org/ContentService/data/query/<stable-id>
Requirements
- Python 3.10+
- Network access to
reactome.org
Procedure
- Run
python3 skills/systems-biology/reactome-event-summary/scripts/fetch_reactome_event_summary.py --stable-id R-HSA-141409 --out skills/systems-biology/reactome-event-summary/assets/r_hsa_141409_summary.json.
- Inspect the output fields:
display_name, schema_class, species, compartments, and summary_text.
- If the stable ID is unknown or invalid, retry with a confirmed public Reactome ID.
Validation
- Command exits successfully.
- Output JSON contains the requested
stable_id and a non-empty display_name.
Failure modes and fixes
- HTTP 404: confirm the stable ID exists and is public in Reactome.
- Empty summary text: some records omit
summation; rely on the other metadata fields.
- Need deeper traversal: build a separate skill around a documented Reactome endpoint first.
Safety and limits
- This skill only uses the documented stable-ID query surface.
- It summarizes one Reactome record at a time and does not resolve downstream pathway structure.
Example
python3 skills/systems-biology/reactome-event-summary/scripts/fetch_reactome_event_summary.py --stable-id R-HSA-141409
Provenance
Related skills
