README.md

Before geting started, please install all packages from the requirementlist

In the home directory, run the following command to initate the server

python api.py

Ways to set up the queries:

In another Command window, run the follwoing comments to get the Knowledge graphs.

Section 1: get the information of KEGG pathways

1: List all the pathway ids and names.

curl http://localhost:5000/PathwayLists/

2: Query the gene list in one pathway(input KEGG id, eg: hsa04010)

curl http://localhost:5000/Pathway/ (eg. http://localhost:5000/Pathway/hsa04010)

Section 2: get the information from the DrugBank

3 Query the target for one drug, return a json file of target genes for the queried drug

curl http://localhost:5000/Query_Targets_by_drug/ (eg. curl http://localhost:5000/Query_Targets_by_drug/Cetuximab)

4 Query the drugs for one target, return a json file of drugs genes for the queried target

curl http://localhost:5000/Query_drugs_by_target// (eg. curl http://localhost:5000/Query_drugs_by_target/EGFR/)

5 Query all FDA approved drugs, return a list of drugs

curl http://localhost:5000/list_FDA_Drugs/

6 Query the KG from Drug-Target-action

Upcoming KGs

Setion 3: SL pairs

7. Query the synthetic lethylity pairs according to gene knockout effects

#curl http://localhost:5000/Query_SL_by_ko/<ko_gene>/ (eg. curl http://localhost:5000/Query_SL_by_ko/EGFR/))

8. Query the synthetic lethylity pairs according to gene mutations

#curl http://localhost:5000/Query_SL_by_mut/<mut_gene>/ (eg. curl http://localhost:5000/Query_SL_by_mut/EGFR/)

Section 4: get the disease associated gene

Section 5: get the gene associated drug

Section 6: get the gene mutation associateed differential gene expression

POST methods: Examples Query how genes show co-expression with another from a gene list curl -X POST -H 'Content-Type: application/json' --data '{"genes":["TP53","FLT3","NPM1","KRAS","NRAS"]}' http://localhost:5000/Query_co_exp_inGroup