Explore biomolecular pathways in the Reactome graph database from the command-line or a Python script.

In addition to biomolecular pathways, Reactome contains expert-authored and peer-reviewed reactions, molecular complex ingredients and structure, and protein-protein interactions.

Reactome also provides links from pathways, reactions, and molecules to biological models, associated research papers, URLs, and books.

1. Run Reactome's Neo4j Tutorial from one of the Jupyter notebooks or a plain Python script

2. Find enriched pathways from the command line, accessing Reactome's online Pathway Analysis Service

3. Write your own Python scripts accessing the Reactome database through Neo4j

• Official Reactome Help

  • Reactome Documentation
  • Support: [email protected]
  • Or open an issue on GitHub like this one or driver

• Unofficial user's download hints

  • 1) Install Neo4j
  • 2) Download Reactome Knowledgebase

• Reactome Publications

  • 2018 | Reactome graph database: Efficient access to complex pathway data

• Reactome Documentation

  • Data Schema
  • Glossary Data Model
  • Icon library
  • Reactome Graph Database on GitHub

• This project uses the Neo4j Python driver that is officially supported by Neo4j

  • https://github.com/neo4j/neo4j-python-driver

Please cite if this repo is used in your research:

Klopfenstein DV, Dampier W ReactomePy Zenodo | (2019) | DOI: 10.5281/zenodo.2634376

@online{klopfenstein2019reactomepy,
  author = {Klopfenstein, DV and 
            Dampier, W},
  title = {ReactomePy},
  year = 2019,
  month = apr,
  url = {https://github.com/dvklopfenstein/ReactomePy},
  doi = {10.5281/zenodo.2634376},
}

Copyright (C) 2018-present, DV Klopfenstein. All rights reserved.