gloriachin/biggimii_api

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