Reactome, Python, and Neo4j

Explore biomolecular pathways in Reactome 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.

Use this Python3 library to:

  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


To Cite

Please cite if this repo is used in your research:

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

BibLaTeX citation

  author = {Klopfenstein, DV and 
            Dampier, W},
  title = {ReactomePy},
  year = 2019,
  month = apr,
  url = {},
  doi = {10.5281/zenodo.2634376},

Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved.