How do I install the Reactome Skill skill?

Run npx skillmds@latest add gabrielmoreira/reactome-skill in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Reactome Skill safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Reactome Skill?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Reactome Skill free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under MIT.

Who published Reactome Skill?

gabrielmoreira (@gabrielmoreira) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Reactome Skill by gabrielmoreira — Agent Skill

Name: Reactome Skill
Rating: 4.2 (5 reviews)
Author: gabrielmoreira

File contents

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.

---name: reactome-skilldescription: 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---> **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`.

Frequently asked questions

Reactome Skill