---
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](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:

```bash
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

```bash
python scripts/reactome_tool.py query_content --id "R-HSA-69278"
```

### 2) Run overrepresentation analysis for a gene list

```bash
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`.

---
Source attribution: aipoch
Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/scientific-skills/Evidence%20Insight/reactome-skill/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 AIpoch

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: aipoch
Original project: https://github.com/aipoch/medical-research-skills/blob/686e09dfdb45d9fa1a08664f06bb93769b3c9d91/scientific-skills/Evidence%20Insight/reactome-skill/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Education & Research
Roles: Business Intelligence Analyst, Data Scientist, Researcher
Specialties: API
Tools: Reactome
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 2d62297b675fb4f0c377f2135df32129486d552ba07a8b62ea549aa1ec028148