Reactome event summary

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

1. 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.
2. Inspect the output fields: display_name, schema_class, species, compartments, and summary_text.
3. 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

• Reactome Content Service docs: https://reactome.org/dev/content-service

Related skills

• ncbi-pubmed-search