Reactome event summary

Skill ma-compbio-lab/SkillFoundry/skills/systems-biology/reactome-event-summary

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill reactome-event-summary

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What its author says it does

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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.

SKILL.md

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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

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

Related skills

ncbi-pubmed-search