CaseOLAP_Pipeline

Implementation of the caseOLAP pipeline for mapping relationships between oxidative stress and drugs.

File overview

neo4j_functions/: Folder containing functions/classes related to use of neo4j
lib/: Folder containing static files like drug lists and oxidative stress markers
Explore_Drug_chemical_OxStress.ipynb: Python notebook to look at reactome pathways related to a curated list of drugs and chemicals related to oxidative stress. Incorporates caseOLAP scores.
Create_Drug_Cooccurance_Graph.ipynb: Creates a neo4J graph relating drug/chemical/pubmid occurances
Export_Subgraph.ipynb: Queries Reactome for relations within 2 edges of drugs in a curated list. Saves a graphml format file.
Import_Subgraph.ipynb: Imports the graphml fromat file in to a new neo4j graph database

Name		Name	Last commit message	Last commit date
Latest commit History 23 Commits
lib		lib
neo4j_functions		neo4j_functions
output		output
.gitignore		.gitignore
1639304259.json		1639304259.json
Create_Drug_Cooccurance_Graph.ipynb		Create_Drug_Cooccurance_Graph.ipynb
Explore_Drug_chemical_OxStress.ipynb		Explore_Drug_chemical_OxStress.ipynb
Export_Subgraph.ipynb		Export_Subgraph.ipynb
Import_Subgraph.ipynb		Import_Subgraph.ipynb
Query_Neo4j_Python.ipynb		Query_Neo4j_Python.ipynb
README.md		README.md
drugbank_targets_reactome.ipynb		drugbank_targets_reactome.ipynb
requirements.txt		requirements.txt