Johnllopez Week 9 - Revision history

Johnllopez616: Added my template

2017-10-31T06:12:02Z

Added my template

Johnllopez616: Fixed the display of JSON

2017-10-31T06:11:16Z

Fixed the display of JSON

Johnllopez616: Added refernces

2017-10-31T06:06:54Z

Added refernces

Johnllopez616: Added acknowledgements

2017-10-31T05:56:45Z

Added acknowledgements

Johnllopez616: Added the deliverable

2017-10-31T05:43:00Z

Added the deliverable

Johnllopez616: Explained how I got final answer

2017-10-31T05:40:16Z

Explained how I got final answer

Johnllopez616: Explained how I got the symbol portion

2017-10-31T05:35:04Z

Explained how I got the symbol portion

Johnllopez616: Added the API Exploration section

2017-10-31T05:14:21Z

Added the API Exploration section

Johnllopez616: Fixed the file

2017-10-30T03:59:52Z

Fixed the file

Johnllopez616: Finished the tests

2017-10-30T03:59:21Z

Finished the tests

← Older revision		Revision as of 06:12, 31 October 2017
Line 72:		Line 72:
	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 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		LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017 from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
		+
		+
		+	{{Template:johnllopez616}}

@@ Line 38: / Line 38: @@
   {"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}
+ {"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}

@@ Line 37: / Line 37: @@
   curl  https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1
-  {"results":[
+  {"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}
@@ Line 63: / Line 62: @@
 ===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.
 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)
-  https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
+===References===

← Older revision		Revision as of 05:56, 31 October 2017
Line 61:		Line 61:

	==Acknowledgements and References==		==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.

		+	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)

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

@@ Line 50: / Line 50: @@
   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"}
+ {"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:
 ==Acknowledgements and References==
   https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

← Older revision		Revision as of 05:40, 31 October 2017
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	curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=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.	+	{"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:
		+
		+

← Older revision		Revision as of 05:35, 31 October 2017
Line 30:		Line 30:
	==API Exploration==		==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:		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
		+
		+	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.

← Older revision		Revision as of 05:14, 31 October 2017
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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:
		+
		+
		+	==Acknowledgements and References==
		+
		+	https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

@@ Line 6: / Line 6: @@
 -genes_31-edges_Schade-data_estimation_output.sif
 -genes_31-edges_Schade-data_estimation_output.xlsx
 -genes_31-edges_Schade-data_estimation_output.graphml