Export Subgraph of Reactome

• This files generates cypher exports of the neighborhood around each drug found in the reactome database related to oxidative stress.
• Files export to [Path_To_Local_Graph_DB]/import/drug_subgraphs/[Drug Name].cypher

import neo4j_functions.driver as neo4j_driver
import pandas as pd
import importlib
import progressbar

drug_pathway_caseolap = pd.read_csv('output/drug_reactome_pathways_caseolap.csv')
drug_pathway_caseolap.head()

# Connect to local Reactome
driver = neo4j_driver.driver(uri = "bolt://localhost:7687", user = "neo4j", password = "Akre1234")

drugs = drug_pathway_caseolap.Drug.unique()
lowered_drugs = [d.lower() for d in drugs]
query = (
"""
CALL apoc.export.graphml.query(
"MATCH (d:Drug)-[a*1..2]-(b) WHERE toLower(d.displayName) IN %s RETURN d,a,b",
"/all_drugs.graphml",
{readLabels:true, storeNodeIds: true}
)

""" % ("['" + "', '".join(lowered_drugs) + "']")
)
print(query)
driver.run_query(query);

CALL apoc.export.graphml.query(
"MATCH (d:Drug)-[a*1..2]-(b) WHERE toLower(d.displayName) IN ['warfarin [cytosol]', 'rivaroxaban [extracellular region]', 'dabigatran [extracellular region]', 'apixaban [extracellular region]', 'edoxaban [extracellular region]', 'carvedilol [extracellular region]', 'propranolol [extracellular region]', 'metoprolol [extracellular region]', 'sotalol [extracellular region]', 'nebivolol [extracellular region]', 'acebutolol [extracellular region]', 'atenolol [extracellular region]', 'betaxolol [extracellular region]', 'esmolol [extracellular region]', 'labetalol [extracellular region]', 'ticagrelor [extracellular region]', 'ticlopidine [extracellular region]', 'clopidogrel [extracellular region]', 'r-138727 [extracellular region]', 'cangrelor [extracellular region]', 'dobutamine [extracellular region]', 'pindolol [extracellular region]', 'isoprenaline [extracellular region]', 'procainamide [extracellular region]', 'lidocaine [extracellular region]', 'disopyramide [extracellular region]', 'quinidine [extracellular region]', 'phenytoin [extracellular region]', 'mexiletine [extracellular region]', 'tocainide [extracellular region]', 'propafenone [extracellular region]', 'flecainide [extracellular region]', 'dofetilide [extracellular region]', 'ibutilide [extracellular region]', 'amlodipine [extracellular region]', 'diltiazem [extracellular region]', 'isradipine [extracellular region]', 'nifedipine [extracellular region]', 'felodipine [extracellular region]', 'nicardipine [extracellular region]', 'nisoldipine [extracellular region]', 'verapamil [extracellular region]', 'captopril [extracellular region]', 'lisinopril [extracellular region]', 'irbesartan [extracellular region]', 'telmisartan [extracellular region]', 'losartan [extracellular region]', 'olmesartan [extracellular region]', 'candesartan [extracellular region]', 'valsartan [extracellular region]', 'benazepril [endoplasmic reticulum lumen]', 'perindopril [endoplasmic reticulum lumen]', 'ramipril [endoplasmic reticulum lumen]', 'quinapril [endoplasmic reticulum lumen]', 'fosinopril [endoplasmic reticulum lumen]', 'enalapril [endoplasmic reticulum lumen]', 'enoximone [cytosol]', 'milrinone [cytosol]'] RETURN d,a,b",
"/all_drugs.graphml",
{readLabels:true, storeNodeIds: true}
)