aipoch/reactome-skill
scientific-skills/Evidence Insights/reactome-skill/SKILL.md
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.
$ install --global
skillsauthnpx skillsauth add aipoch/medical-research-skills reactome-skillInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- 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
- skill-author:
- AIPOCH
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
reactome2pyand/or direct HTTP calls withrequests) 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-xxxxxfor 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.
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