Difference between revisions of "Johnllopez Week 9"
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# All 3 tests pass successfully. | # All 3 tests pass successfully. | ||
# All 3 tests pass successfully. | # All 3 tests pass successfully. | ||
+ | |||
+ | ==API Exploration== | ||
+ | In order to complete this portion of the assignment, I met with my partner, [[User:Hhinsch| Hayden Hinsch]], as well as [[User:Dbashour | Dina Bashoura]] and [[User:Simonwro120 | 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 [[User:Hhinsch| Hayden Hinsch]]. We met on Sunday to do the tests together and confirm that we had the same results. On Monday, I worked with [[User:Hhinsch| Hayden Hinsch]],[[User:Dbashour | Dina Bashoura]] and [[User:Simonwro120 | Simon Wroblewski]] in the lab. We shared ideas about the project and inspected the JSON together. | ||
+ | |||
+ | I also used my lifeline, where [[User:Dondi|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. | ||
+ | [[User:Johnllopez616|Johnllopez616]] ([[User talk: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 | ||
+ | |||
+ | |||
+ | {{Template:johnllopez616}} |
Latest revision as of 06:12, 31 October 2017
Contents
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
- This test passes successfully.
- This test passes successfully.
- This test passes successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- All 3 tests pass successfully.
- All 3 tests pass successfully.
- All 3 tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- Both tests pass successfully.
- All 3 tests pass successfully.
- All 3 tests pass successfully.
- 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
Individual Journal Entries and Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 14
- Week 15
Class Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 14
- Week 15
Class Weekly Journal Entries / Project Weekly Journal Entries
- Class Weekly Journal 1
- Class Weekly Journal 2
- Class Weekly Journal 3
- Class Weekly Journal 4
- Class Weekly Journal 5
- Class Weekly Journal 6
- Class Weekly Journal 7
- Class Weekly Journal 8
- Class Weekly Journal 9
- Class Weekly Journal 10
- Class Weekly Journal 11
- Project Journal Week 12
- Project Journal Week 14
- Project Journal Week 15
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