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.