Agent Skills

Reactome Skill

AIPOCH

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.

3
0
FILES
reactome-skill/
skill.md
scripts
reactome_tool.py
references
api_reference.md
skill_spec.yaml
92100Total Score
View Evaluation Report
Core Capability
85 / 100
Functional Suitability
11 / 12
Reliability
9 / 12
Performance & Context
8 / 8
Agent Usability
14 / 16
Human Usability
8 / 8
Security
9 / 12
Maintainability
9 / 12
Agent-Specific
17 / 20
Medical Task
20 / 20 Passed
100You have a list of genes/proteins and want to run pathway overrepresentation (enrichment) analysis against Reactome
4/4
97You need to retrieve curated pathway content (hierarchy, reactions, participants) by Reactome stable IDs (e.g., R-HSA-69278)
4/4
95Pathway enrichment (overrepresentation) for identifier lists
4/4
94Expression analysis by mapping expression data to Reactome pathways
4/4
94End-to-end case for Pathway enrichment (overrepresentation) for identifier lists
4/4

SKILL.md

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.