Johnllopez Week 9

GRNSight Testing

Below is a list of the test results for the Normalization and Zoom functions.

We used the following files for the tests:

21-genes_31-edges_Schade-data_estimation_output.sif
21-genes_31-edges_Schade-data_estimation_output.xlsx
21-genes_31-edges_Schade-data_estimation_output.graphml

1. This test passes successfully.
2. This test passes successfully.
3. This test passes successfully.
4. Both tests pass successfully.
5. Both tests pass successfully.
6. Both tests pass successfully.
7. Both tests pass successfully.
8. Both tests pass successfully.
9. Both tests pass successfully.
10. All 3 tests pass successfully.
11. All 3 tests pass successfully.
12. All 3 tests pass successfully.
13. Both tests pass successfully.
14. Both tests pass successfully.
15. Both tests pass successfully.
16. All 3 tests pass successfully.
17. All 3 tests pass successfully.
18. All 3 tests pass successfully.

API Exploration

In order to complete this portion of the assignment, I met with my partner, Hayden Hinsch, as well as Dina Bashoura and Simon Wroblewski in the lab. I developed my answer by first inspecting the URL given for the original JSON:

curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=1012319

I then inspected the JSON, and I saw that there were several parameters within the JSON, including an ID parameter as well as a symbol parameter. Thus, I changed my URL to search using the symbol parameter instead of the ID, and I got the following results when I tested for BRO1:

curl  https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1

The output came to be two "results" objects, one of which was exactly the same as the one I retrieved from inputting the Gene ID. I knew I was close but I needed a way to filter my results.

Acknowledgements and References

https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7