Zvanysse Week 9

URL

http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?' -H 'Content-type:application/json'

Note: an explanation is provided in the Electronic Workbook.

Electronic workbook

First, we downloaded three files with different file extensions: .xlsx, .graphml, and .sif. The three files are:

Note how these are the same files as my homework partner, Antonia Porras.

Test 1

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test PASSED with no errors.

Test 2

First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test PASSED with no errors.

Test 3

First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test PASSED with no errors.

Test 4

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test FAILED with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image:

Test 5

First, we went to GRNsight and imported the Sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test FAILED with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image:

Test 6

First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test FAILED with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image:

Test 7

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 8

First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 9

First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 10

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

Test 11

First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

Test 12

First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

Test 13

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 14

First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 15

First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test PASSED with no errors.

Test 16

First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

Test 17

First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

Test 18

First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test PASSED with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

URL Explanation

First, I decided to go from the middle out. At first, I noticed that I could just change the ID name in this URL: "http://rest.ensembl.org/lookup/id/YPL084W?content-type=application/json;expand=1" however this does not get from the actual name "BRO1" to the relevant information. So I browsed the API dictionary knowing that I had to use both "BRO1" and "saccharomyces_cerevisiae" in the URL. I came across a lookup guide that takes in the Gene name and related species and spews out the information on that gene. This is how I arrived at this part of the URL: "http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?" The next part was figuring out the content-type=application/json part. This is basically just a necessary logistical part that lets the service know that the user wants a json format. "expand=1" basically expands the information into more data. I wasn't sure if it was necessary, but the data was relevant so I decided to go forth and add it in.

type in http://rest.ensembl.org/lookup/symbol/
Type in the relevant species followed by a "/" Example: "saccharomyces_cerevisiae/"
Type in the desired gene symbol followed by a question mark, i.e. "BRO1?"
For json users, type in content-type=application/json
If you would like to know more data, place a semi-colon after "json" and type "expand=1"

Here is the URL:
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1

Alternatively, we can use the curl method to retrieve the data, it is pretty much the same except that the syntax is a little different. First, add "curl" to the beginning of it and separate the URL before the "content-type." instead, type " -H " and then type the "content-type=application/json;" Not that there is not a need for the expand=1;
Here is the curl function:
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?' -H 'Content-type:application/json'

Acknowledgments

I worked with Antonio Porras to complete the test cases.
I consulted with Arash on clarifying what the URL question was asking
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Zvanysse (talk) 00:33, 30 October 2017 (PDT)

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Zvanysse

BIOL/CMSI 367-01: Biological Databases Fall 2017

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