Agent skill · research science · google-deepmind
reactome-database
Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.
Why this skill is useful
Provides specific commands and procedures for querying the Reactome database that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 5k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
Reactome Analysis & Content Service Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/reactomedatabaseLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://reactome.org/license and https://reactome.org/cite, then (2) create the file recording the notification text and timestamp. Overview Reactome is a free, open-source, curated pathway database. This skill wraps both the Analysis Service (https://reactome.org/AnalysisService/) and the Content Service (https://reactome.org/ContentService/) providing pathway enrichment analysis, identifier mapping, reaction details, pathway hierarchy navigation, diagram export, cross-reference mapping, and search. When to Use This Skill Performing pathway enrichment (overrepresentation) analysis on gene/protein lists Retrieving analysis results using a token from previous enrichment Identifying which genes or proteins were not found in a pathway analysis Analyzing gene expression data against pathway annotations Mapping identifiers to Reactome entities across species Retrieving reaction participants (inputs, outputs, catalysts, regulators) Navigating pathway hierarchy and listing top-level pathways Finding which complexes or sets contain a protein Exporting pathway/reaction diagrams (PNG/SVG) with gene highlighting Cross-referencing identifiers across databases (UniProt, Ensembl, etc.) Searching the Reactome knowledgebase Downloading analysis reports (PDF, CSV, JSON) Comparing pathways across species Common Species IDs Reference list for common research organisms: Homo sapiens ID: 9606 Mus musculus (Mouse) ID: 48892 Rattus norvegicus (Rat) ID: 48895 Common Pathway IDs Reference list for commonly used Reactome pathway stable IDs: Cell Cycle Stable ID: R-HSA-1640170 Notes: Top-level pathway (broad) Cell Cycle, Mitotic Stable ID: R-HSA-69278 Notes: Specific sub-pa …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/reactome_database