Agent skill · research science · aiskillstore
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
Why this skill is useful
Provides specific API commands and analysis methods for querying and analyzing biological pathways that the AI wouldn't reliably generate on its own.
What it needs
Requires reactome2py installed locally. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
Reactome Database Overview Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research. When to Use This Skill This skill should be used when: Performing pathway enrichment analysis on gene or protein lists Analyzing gene expression data to identify relevant biological pathways Querying specific pathway information, reactions, or molecular interactions Mapping genes or proteins to biological pathways and processes Exploring disease-related pathways and mechanisms Visualizing analysis results in the Reactome Pathway Browser Conducting comparative pathway analysis across species Core Capabilities Reactome provides two main API services and a Python client library: 1. Content Service - Data Retrieval Query and retrieve biological pathway data, molecular interactions, and entity information. Common operations: Retrieve pathway information and hierarchies Query specific entities (proteins, reactions, complexes) Get participating molecules in pathways Access database version and metadata Explore pathway compartments and locations API Base URL: https://reactome.org/ContentService 2. Analysis Service - Pathway Analysis Perform computational analysis on gene lists and expression data. Analysis types: Overrepresentation Analysis: Identify statistically significant pathways from gene/protein lists Expression Data Analysis: Analyze gene expression datasets to find relevant pathways Species Comparison: Compare pathway data across different organisms API Base URL: https://reactome.org/AnalysisService 3. reactome2py Python Package Python client library that wraps Reactome API calls for easier programmatic access. Installation: Note: The reactome2py package (version 3.0.0, released January 2021) is functional but not actively maintained. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/reactome-database--0811c5