reactome-database

Reactome Analysis & Content Service

Prerequisites

1. `uv`: Read the uv skill and follow its Setup instructions to ensure

uv is installed and on PATH.

1. 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-pathway — use this for diagrams and drill-downs
• Immune System
• Stable ID: R-HSA-168256
• Notes: Top-level pathway
• Signal Transduction
• Stable ID: R-HSA-162582
• Notes: Top-level pathway
• Gene Expression
• Stable ID: R-HSA-74160
• Notes: Top-level pathway
• Programmed Cell Death
• Stable ID: R-HSA-5357801
• Notes: Top-level pathway

Important: When the user asks for a "Cell Cycle" diagram or analysis, prefer the specific Cell Cycle, Mitotic pathway (R-HSA-69278) unless the user explicitly requests the top-level overview. The examples throughout this document use R-HSA-69278.

Core Rules

1. Always use `--output`: Every subcommand requires --output <file> to

write results to a file. Never rely on stdout for large results.

1. Default species is Homo sapiens: Use --species to override.
2. Tokens expire after 7 days: Store tokens from analysis results to

retrieve them later without re-submitting data.

1. Use `--fdr` and `--pvalue` to filter: Enrichment results can be

overwhelming. Filter with --fdr 0.05 or --pvalue 0.01 to focus on statistically significant pathways.

1. Identifier formats: Reactome auto-detects identifiers including gene

symbols (TP53), UniProt (P04637), Ensembl (ENSG00000141510), ChEBI, OMIM, EntrezGene, and many more.

1. Handle large outputs: For commands that return large data (like

species-comparison), use the --summary flag to truncate lists and avoid exceeding workspace file size limits (1MB).

1. Notification: If this skill is used, ensure this is mentioned in the

output.

Tool Execution

The CLI tool is at scripts/reactome_analysis.py. Run with uv:

uv run scripts/reactome_analysis.py <command> [options] --output /tmp/out.json

To list all available subcommands and flags, run:

uv run scripts/reactome_analysis.py --help

Use --help to verify available subcommands or flags before executing an unfamiliar command.

Feature Domains

1. Database Info

uv run scripts/reactome_analysis.py db-version --output /tmp/version.json
uv run scripts/reactome_analysis.py db-name --output /tmp/name.json

2. Single Identifier Analysis

uv run scripts/reactome_analysis.py identifier --id TP53 --output /tmp/tp53.json
uv run scripts/reactome_analysis.py identifier-projection --id TP53 --output /tmp/tp53_proj.json

3. Batch Analysis (Enrichment)

Submit a list of identifiers for overrepresentation or expression analysis:

uv run scripts/reactome_analysis.py analyze --data "TP53,BRCA1,EGFR" --output /tmp/enrich.json
uv run scripts/reactome_analysis.py analyze --file genes.txt --output /tmp/enrich.json
uv run scripts/reactome_analysis.py analyze-projection --data "TP53,BRCA1" --output /tmp/proj.json
uv run scripts/reactome_analysis.py analyze --data "TP53,BRCA1" --fdr 0.05 --output /tmp/sig.json

Common options: --page-size (alias --limit), --page (alias --offset), --sort-by, --order, --resource, --species, --fdr, --pvalue.

4. Token-Based Result Retrieval

uv run scripts/reactome_analysis.py token-result --token TOKEN --output /tmp/result.json
uv run scripts/reactome_analysis.py token-not-found --token TOKEN --output /tmp/notfound.json
uv run scripts/reactome_analysis.py token-resources --token TOKEN --output /tmp/resources.json
uv run scripts/reactome_analysis.py token-found-entities --token TOKEN --pathway R-HSA-69278 --output /tmp/found.json
uv run scripts/reactome_analysis.py token-filter-species --token TOKEN --species-filter 9606 --output /tmp/filtered.json
uv run scripts/reactome_analysis.py token-reactions-pathway --token TOKEN --pathway R-HSA-69278 --output /tmp/rxns.json

5. Download Results

uv run scripts/reactome_analysis.py download-result --token TOKEN --output /tmp/full.json
uv run scripts/reactome_analysis.py download-pathways --token TOKEN --output /tmp/pathways.csv
uv run scripts/reactome_analysis.py download-found --token TOKEN --output /tmp/found.csv
uv run scripts/reactome_analysis.py download-not-found --token TOKEN --output /tmp/notfound.csv

6. Identifier Mapping

uv run scripts/reactome_analysis.py mapping --data "TP53,BRCA1" --output /tmp/mapped.json
uv run scripts/reactome_analysis.py mapping-projection --data "TP53" --output /tmp/mapped_proj.json

7. Reaction Participants & Mechanism of Action

Retrieve the molecular participants of a reaction (inputs, outputs, catalysts):

uv run scripts/reactome_analysis.py participants --id R-HSA-6804194 --output /tmp/participants.json
uv run scripts/reactome_analysis.py participating-entities --id R-HSA-6804194 --output /tmp/entities.json

8. Complex & Set Membership

Find which complexes or sets contain a given entity:

uv run scripts/reactome_analysis.py component-of --id R-HSA-69488 --output /tmp/complexes.json

9. Pathway Hierarchy Navigation

Move up (ancestors) or down (contained events) the pathway hierarchy:

uv run scripts/reactome_analysis.py event-ancestors --id R-HSA-69278 --output /tmp/ancestors.json
uv run scripts/reactome_analysis.py contained-events --id R-HSA-69278 --output /tmp/steps.json
uv run scripts/reactome_analysis.py top-pathways --output /tmp/top.json
uv run scripts/reactome_analysis.py low-pathways --id R-HSA-69488 --output /tmp/low.json

10. Diagram Export

Export pathway or reaction diagrams as PNG/SVG, with optional gene highlighting:

uv run scripts/reactome_analysis.py diagram --id R-HSA-69278 --output /tmp/diagram.png
uv run scripts/reactome_analysis.py diagram --id R-HSA-69278 --highlight TP53 --output /tmp/highlighted.png
uv run scripts/reactome_analysis.py diagram --id R-HSA-69278 --format svg --output /tmp/diagram.svg
uv run scripts/reactome_analysis.py reaction-diagram --id R-HSA-6804194 --output /tmp/rxn.png

11. Cross-Reference Mapping

Resolve identifiers to Reactome internal IDs and cross-references:

uv run scripts/reactome_analysis.py xref-mapping --id TP53 --output /tmp/xref.json
uv run scripts/reactome_analysis.py xref-mapping-batch --data "TP53,BRCA1" --output /tmp/xrefs.json

12. Search

uv run scripts/reactome_analysis.py search --query "TP53 apoptosis" --output /tmp/results.json

13. Query Entry by ID

uv run scripts/reactome_analysis.py query --id R-HSA-69278 --output /tmp/entry.json

14. Report & Species Comparison

uv run scripts/reactome_analysis.py report --token TOKEN --output /tmp/report.pdf
uv run scripts/reactome_analysis.py species-comparison --species-id 48892 --output /tmp/species.json
# Use --summary to truncate large output and avoid workspace file size limits
uv run scripts/reactome_analysis.py species-comparison --species-id 48892 --summary --output /tmp/species.json

Recipe: Interpreting Gene Set Enrichment

A step-by-step workflow for interpreting gene set enrichment results:

1. Submit gene list with projection to human pathways: `bash uv run

scripts/reactome_analysis.py analyze-projection \ --data "TP53,BRCA1,EGFR,MYC,PTEN" --fdr 0.05 --output /tmp/enrichment.json`

1. Inspect top pathways — examine pathwaysFound, top pathway names,

p-values, and FDR values in the output.

1. Drill into a pathway — get its sub-events and reaction details: `bash uv

run scripts/reactomeanalysis.py contained-events --id R-HSA-69278 --output /tmp/steps.json uv run scripts/reactomeanalysis.py participants --id <reaction_id> --output /tmp/parts.json`

1. Visualise — export a diagram with your genes highlighted: `bash uv run

scripts/reactome_analysis.py diagram --id R-HSA-69278 \ --highlight "TP53,BRCA1" --output /tmp/diagram.png`

1. Check hierarchy — navigate up to see broader biological context: `bash

uv run scripts/reactome_analysis.py event-ancestors --id R-HSA-69278 --output /tmp/ancestors.json`

1. Cross-reference — map identifiers to other databases: `bash uv run

scripts/reactome_analysis.py xref-mapping --id TP53 --output /tmp/xrefs.json`

Reference

For detailed API endpoint documentation, see references/api_reference.md.