https://github.com/dvklopfenstein/reactomepy

Explore biomolecular pathways in Reactome from the command-line or a Python script
https://github.com/dvklopfenstein/reactomepy

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool biological-networks biotech biotechnology molecular-biology pathway-analysis pathway-enrichment-analysis pathway-models protein-protein-interaction reactome reactome-pathway

Last synced: about 2 months ago
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Explore biomolecular pathways in Reactome from the command-line or a Python script

Host: GitHub
URL: https://github.com/dvklopfenstein/reactomepy
Owner: dvklopfenstein
License: agpl-3.0
Created: 2018-09-28T23:21:33.000Z (over 6 years ago)
Default Branch: main
Last Pushed: 2024-10-12T20:39:42.000Z (7 months ago)
Last Synced: 2025-03-18T02:12:59.688Z (2 months ago)
Topics: bioinformatics, bioinformatics-analysis, bioinformatics-pipeline, bioinformatics-scripts, bioinformatics-tool, biological-networks, biotech, biotechnology, molecular-biology, pathway-analysis, pathway-enrichment-analysis, pathway-models, protein-protein-interaction, reactome, reactome-pathway
Language: Python
Homepage:
Size: 17.1 MB
Stars: 22
Watchers: 1
Forks: 4
Open Issues: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

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README

        # [Reactome](https://reactome.org/), Python, and Neo4j

[![DOI](doc/images/badge_zenodo.2634376.svg)](https://doi.org/10.5281/zenodo.2634377)

[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

[![Latest PyPI version](https://img.shields.io/pypi/v/ReactomePy.svg)](https://pypi.python.org/pypi/ReactomePy)

[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/version.svg)](https://anaconda.org/dvklopfenstein/reactomepy)

[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/latest_release_date.svg)](https://anaconda.org/dvklopfenstein/reactomepy)

[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/platforms.svg)](https://anaconda.org/dvklopfenstein/reactomepy)

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

## Reactome

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**](https://reactome.org/dev/graph-database/extract-participating-molecules)

     from one of the [**Jupyter notebooks**](/notebooks/tutorial/README.md)

     or a plain [**Python script**](/src/bin_neo4j/tutorial)

  2) Find enriched pathways

     [**from the command line**](/doc/md/README_analyses.md),

     accessing Reactome's online

     [**Pathway Analysis Service**](https://reactome.org/AnalysisService/) 

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

## Links

  * **Official Reactome Help**

    * [**Reactome Documentation**](https://reactome.org/dev/graph-database)    

    * Support: **[email protected]**

    * Or open an issue on GitHub like [this one](https://github.com/neo4j/neo4j/issues/12408) or [driver](https://github.com/neo4j/neo4j-python-driver/issues/365)

  * **Unofficial user's download hints**

    * [1) Install Neo4j](/doc/md/README_install_neo4j.md)    

    * [2) Download Reactome Knowledgebase](/doc/md/README_download_hints.md)   

  * **Reactome Publications**

    * 2018 | [Reactome graph database: Efficient access to complex pathway data](https://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1005968)

  * **Reactome Documentation**    

    * [Data Schema](https://reactome.org/content/schema/DatabaseObject)    

    * [Glossary Data Model](http://wiki.reactome.org/index.php/Glossary_Data_Model)    

    * [Icon library](https://reactome.org/icon-lib)    

    * [Reactome Graph Database on GitHub](https://github.com/reactome/graph-core)    

  * This project uses the **Neo4j Python driver** that is [officially supported](https://neo4j.com/developer/python) by Neo4j

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

## To Cite

_Please cite if this repo is used in your research_:

Klopfenstein DV, Dampier W [_ReactomePy_](https://doi.org/10.5281/zenodo.2634376)

_Zenodo_ | (2019) | DOI: 10.5281/zenodo.2634376

### BibLaTeX citation

```

@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.

ecosyste.ms

Data

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Indexes

Applications

Experiments

Awesome

https://github.com/dvklopfenstein/reactomepy

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README