Mapping drug targets on KEGG pathway

Here we show a example of data integration. We map drug targets(from Drugbank) on KEGG pathway. To manage several tables, we use MongoDB and PyMongo.

Importing all data into MongoDB

First we export node attribute table of Alanine, aspartate and glutamate metabolism as alanine_nodes.csv.

Next we download drug targets from Drugbank and id convert table with KEGG REST API.

wget http://www.drugbank.ca/system/downloads/current/all_target_ids_all.csv.zip
unzip all_target_ids_all.csv.zip
wget http://rest.kegg.jp/conv/eco/uniprot
mv uniprot conv_eco_uniprot.tsv

Finally we import these tables into mongodb.

mongoimport --db keggscape --collection alanine_nodes --headerline --type csv --file alanine_nodes.csv
mongoimport --db keggscape --collection all_target_ids_all --headerline --type csv --file all_target_ids_all.csv
mongoimport --db keggscape --collection conv_eco_uniprot -f uniprot_id,kegg_id --type tsv --file conv_eco_uniprot.tsv

Merging tables with PyMongo

We integrate the three table(network nodes, drug targets table, id conversion table). Here we append columns drug target and drug to Cytoscape’s node table.

from pymongo import MongoClient

client = MongoClient()
db = client['keggscape']

node_collection = db['alanine_nodes']
drug_collection = db['all_target_ids_all']
conv_collection = db['conv_eco_uniprot']

gene_table = node_collection.find({"KEGG_NODE_TYPE": "gene"})

for genes in gene_table:
    locuses = genes["KEGG_ID"].split("\r") #newline character depends on your OS, I exported cytoscape table on Mac
    for locus in locuses:
        ids = conv_collection.find_one({"kegg_id": locus})
        drug = drug_collection.find_one({"UniProt ID": ids["uniprot_id"].replace("up:", "")})
        if drug != None:
            node_collection.update({"_id": genes["_id"]}, {"$push": {"drug_ids": drug["Drug IDs"], "target_id": drug["ID"], "target": locus}})
            node_collection.update({"_id": genes["_id"]}, {"$set": {"is_target": 1}})

Next we create fields.txt to export the new node table.

shared name
drug_ids
target_id
target
is_target

and export node table as csv.

mongoexport --db keggscape --collection alanine_nodes --csv --fieldFile fields.txt --out alanine_drugs.csv

import this alanine_drugs.csv into Cytoscape and highlight drug targets as below.