Reactome pathway hierarchy walk starter

Skill ma-compbio-lab/SkillFoundry/skills/systems-biology/reactome-pathway-hierarchy-walk-starter

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

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill reactome-pathway-hierarchy-walk-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.2 KB, 287 tokens by cl100k_base, as published. Nobody here has run it

Reactome Pathway Hierarchy Walk Starter

Use this skill to traverse the official Reactome pathway hierarchy and summarize the ancestor chain, direct children, and descendant count for a target stable ID.

What it does

Fetches the official Reactome eventsHierarchy tree for a species.
Locates a target pathway or reaction stable ID inside the nested hierarchy.
Exports a compact JSON summary with the ancestor path and subtree shape.

When to use it

You need a verified starter for pathway traversal and hierarchy walks.
You want a lightweight way to place a Reactome stable ID inside its broader biological context.
You need deterministic JSON for tests, demos, or downstream routing logic.

Example

python3 skills/systems-biology/reactome-pathway-hierarchy-walk-starter/scripts/run_reactome_hierarchy_walk.py \
  --species 9606 \
  --stable-id R-HSA-141409 \
  --out scratch/reactome-hierarchy/r_hsa_141409_hierarchy.json

Verification