name: reactome-skill
description: Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.
license: MIT
author: AIPOCH
Source: https://github.com/aipoch/medical-research-skills
When to Use
- You have a list of genes/proteins and want to run pathway overrepresentation (enrichment) analysis against Reactome.
- You need to retrieve curated pathway content (hierarchy, reactions, participants) by Reactome stable IDs (e.g.,
R-HSA-69278).
- You want to map expression values onto pathways to support pathway-level interpretation.
- You need to project pathways across species/organisms using Reactome’s species projection capabilities.
- You are building a systems biology workflow that requires programmatic access to Reactome via its REST API.
Key Features
- Pathway enrichment (overrepresentation) for identifier lists.
- Expression analysis by mapping expression data to Reactome pathways.
- Content retrieval for pathways, reactions, and participating molecules.
- Pathway hierarchy access to navigate curated pathway structures.
- Species projection to map pathways across organisms.
- API documentation reference: see
references/api_reference.md.
Dependencies
python (3.x)requests (latest compatible)reactome2py (latest compatible)
Install:
uv pip install reactome2py requests
Example Usage
The following commands are runnable examples using the provided CLI script.
1) Query pathway content by Reactome ID
python scripts/reactome_tool.py query_content --id "R-HSA-69278"
2) Run overrepresentation analysis for a gene list
python scripts/reactome_tool.py analyze_identifiers --identifiers "TP53,BRCA1"
Implementation Details
- API access pattern: The skill uses the Reactome REST API (via
reactome2py and/or direct HTTP calls with requests) to fetch pathway content and submit analyses.
- Identifier input: Gene/protein identifiers are provided as a comma-separated string (e.g.,
TP53,BRCA1) and are submitted for overrepresentation analysis.
- Stable IDs: Content retrieval expects Reactome stable identifiers (commonly formatted like
R-HSA-xxxxx for human pathways).
- Outputs: Results typically include pathway/reaction metadata and analysis outputs (e.g., enriched pathways with associated statistics), depending on the invoked action.
- Reference: Reactome developer documentation is available at https://reactome.org/dev and the local API notes at
references/api_reference.md.