Johnllopez Week 9

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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

{"results":[ {"symbol":"BRO1","length":2535,"scoreType":null,"description":"Cytoplasmic class E vacuolar protein sorting (VPS) factor; coordinates deubiquitination in the multivesicular body (MVB) pathway by recruiting Doa4p to endosomes","jasparAccession":null,"primaryIdentifier":"S000006005","cytoLocation":null,"score":null,"jasparFamily":null,"sgdAlias":"LPF2 ASI6 NPI3 VPS31","qualifier":"Verified","functionSummary":null,"phenotypeSummary":null,"featureType":"ORF","name":"BCK1-like Resistance to Osmotic shock","featAttribute":null,"secondaryIdentifier":"YPL084W","id":1015987,"jasparClass":null,"briefDescription":"Cytoplasmic class E vacuolar protein sorting (VPS) factor","status":"Active"},
{"symbol":"BRO1","length":null,"scoreType":null,"description":null,"jasparAccession":null,"primaryIdentifier":"orf19.1670","cytoLocation":null,"score":null,"jasparFamily":null,"sgdAlias":"orf19.9239 IPF25590.1 IPF8087.2 Contig4-3069_0020 orf6.5745 CA3475 CaO19.9239 CaO19.1670","qualifier":null,"functionSummary":null,"phenotypeSummary":null,"featureType":null,"name":null,"featAttribute":null,"secondaryIdentifier":null,"id":66043773,"jasparClass":null,"briefDescription":"Class E vacuolar protein sorting factor; role in transport from multivesicular body to vacuole; not involved in Rim101 pathway; macrophage and pseudohyphal-repressed; flow model biofilm induced","status":null}

],"executionTime":"2017.10.30 15:58::21","wasSuccessful":true,"error":null,"statusCode":200}

The output came to be two objects within the results array. However, I was unsure which one I needed. I knew I was close but I needed a way to filter my results.

It was then that I used my lifeline to figure out which one of the "results" I needed.

I was given the hint to focus upon the "primaryIdentifier" which begins with an S. Therefore, my final result needed to have a primary identifier that began with S. I decided to use a grep command to obtain that result. 

curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 | grep '"primaryIdentifier":"S'

{"symbol":"BRO1","length":2535,"scoreType":null,"description":"Cytoplasmic class E vacuolar protein sorting (VPS) factor; coordinates deubiquitination in the multivesicular body (MVB) pathway by recruiting Doa4p to endosomes","jasparAccession":null,"primaryIdentifier":"S000006005","cytoLocation":null,"score":null,"jasparFamily":null,"sgdAlias":"LPF2 ASI6 NPI3 VPS31","qualifier":"Verified","functionSummary":null,"phenotypeSummary":null,"featureType":"ORF","name":"BCK1-like Resistance to Osmotic shock","featAttribute":null,"secondaryIdentifier":"YPL084W","id":1015987,"jasparClass":null,"briefDescription":"Cytoplasmic class E vacuolar protein sorting (VPS) factor","status":"Active"}

This result was what I needed to confirm that the following URL is the solution:

Deliverable

Let x = gene symbol 

curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=x | grep '"primaryIdentifier":"S'


Acknowledgements and References

Acknowledgements

For the first part of the assignment, I worked with my partner Hayden Hinsch. We met on Sunday to do the tests together and confirm that we had the same results. On Monday, I worked with Hayden Hinsch, Dina Bashoura and Simon Wroblewski in the lab. We shared ideas about the project and inspected the JSON together.

I also used my lifeline, where Dondi provided the clarification for a question.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Johnllopez616 (talk) 22:56, 30 October 2017 (PDT)

References

FlymineAPI. (2017). Retrieved October 30, 2017 from http://iodocs.apps.intermine.org/flymine/docs#/
LMU BioDB 2017. (2017). Week 7. Retrieved October 30, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
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