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[Reactome](https://reactome.org/), Python, and Neo4j\n[![DOI](doc/images/badge_zenodo.2634376.svg)](https://doi.org/10.5281/zenodo.2634377)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Latest PyPI version](https://img.shields.io/pypi/v/ReactomePy.svg)](https://pypi.python.org/pypi/ReactomePy)\n[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/version.svg)](https://anaconda.org/dvklopfenstein/reactomepy)\n[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/latest_release_date.svg)](https://anaconda.org/dvklopfenstein/reactomepy)\n[![Anaconda-Server Badge](https://anaconda.org/dvklopfenstein/reactomepy/badges/platforms.svg)](https://anaconda.org/dvklopfenstein/reactomepy)\n\nExplore biomolecular pathways in the Reactome graph database from the command-line or a Python script.    \n\n## Reactome\n\nIn addition to biomolecular pathways,\nReactome contains \nexpert-authored and peer-reviewed\nreactions, \nmolecular complex ingredients and structure, and\nprotein-protein interactions.\n\nReactome also provides links from pathways, reactions, and molecules to \nbiological models, associated research papers, URLs, and books.\n\n\n## Use this Python3 library to:\n\n  1) Run [**Reactome's Neo4j Tutorial**](https://reactome.org/dev/graph-database/extract-participating-molecules)\n     from one of the [**Jupyter notebooks**](/notebooks/tutorial/README.md)\n     or a plain [**Python script**](/src/bin_neo4j/tutorial)\n\n  2) Find enriched pathways\n     [**from the command line**](/doc/md/README_analyses.md),\n     accessing Reactome's online\n     [**Pathway Analysis Service**](https://reactome.org/AnalysisService/) \n\n  3) Write your own Python scripts accessing the Reactome database through Neo4j\n\n\n## Links\n  * **Official Reactome Help**\n    * [**Reactome Documentation**](https://reactome.org/dev/graph-database)    \n    * Support: **help@reactome.org**\n    * 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)\n\n  * **Unofficial user's download hints**\n    * [1) Install Neo4j](/doc/md/README_install_neo4j.md)    \n    * [2) Download Reactome Knowledgebase](/doc/md/README_download_hints.md)   \n  * **Reactome Publications**\n    * 2018 | [Reactome graph database: Efficient access to complex pathway data](https://journals.plos.org/ploscompbiol/article?rev=2\u0026id=10.1371/journal.pcbi.1005968)\n  * **Reactome Documentation**    \n    * [Data Schema](https://reactome.org/content/schema/DatabaseObject)    \n    * [Glossary Data Model](http://wiki.reactome.org/index.php/Glossary_Data_Model)    \n    * [Icon library](https://reactome.org/icon-lib)    \n    * [Reactome Graph Database on GitHub](https://github.com/reactome/graph-core)    \n\n  * This project uses the **Neo4j Python driver** that is [officially supported](https://neo4j.com/developer/python) by Neo4j\n    * https://github.com/neo4j/neo4j-python-driver\n\n## To Cite\n\n_Please cite if this repo is used in your research_:\n\nKlopfenstein DV, Dampier W [_ReactomePy_](https://doi.org/10.5281/zenodo.2634376)\n_Zenodo_ | (2019) | DOI: 10.5281/zenodo.2634376\n\n### BibLaTeX citation\n\n```\n@online{klopfenstein2019reactomepy,\n  author = {Klopfenstein, DV and \n            Dampier, W},\n  title = {ReactomePy},\n  year = 2019,\n  month = apr,\n  url = {https://github.com/dvklopfenstein/ReactomePy},\n  doi = {10.5281/zenodo.2634376},\n}\n```\n\nCopyright (C) 2018-present, DV Klopfenstein. All rights reserved.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdvklopfenstein%2Freactomepy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdvklopfenstein%2Freactomepy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdvklopfenstein%2Freactomepy/lists"}