Hhinsch Week 9
From LMU BioDB 2017
Contents
GRNsight Client Side Testing Document: Normalization + Zoom and Web Service API Exploration
GRNsight Client Side Testing Document: Normalization + Zoom
- We used the following files for our tests:
21-genes_31-edges_Schade-data_estimation_output.xlsx
21-genes_31-edges_Schade-data_estimation_output.sif
21-genes_31-edges_Schade-data_estimation_output.graphml
| Test | Pass or Fail | Additional Explanation |
|---|---|---|
| Test 1 | Pass | There weren't any errors in completing this process. |
| Test 2 | Pass | There weren't any errors in completing this process. |
| Test 3 | Pass | There weren't any errors in completing this process. The graph showed up completely grey in the other two .graphml files.
|
| Test 4 | Pass | There weren't any errors. I used the edge weight factor of one and the lines became very thick. |
| Test 5 | Pass | I imported the .sif file and changed the weight factor from 1 to 2. It should be noted that the edge weight factor stays the same as when you determined it in the step before, even if you import a new graph.
|
| Test 6 | Pass | For this .graphml file it uploaded then I changed the edge weight factor to 0.001 and it worked. There isn't any way to set the normative factor for the other two .graphml files.
|
| Test 7 | Pass | The graph zoomed without a problem. |
| Test 8 | Pass | The graph zoomed without a problem. |
| Test 9 | Pass | The graph zoomed without a problem. |
| Test 10 | Pass | I set the normalization factor to 0.001. The graph zoomed without a problem.
|
| Test 11 | Pass | I set the normalization factor to 0.001. The graph zoomed without a problem.
|
| Test 12 | Pass | I set the normalization factor to 0.001. The graph zoomed without a problem.
|
| Test 13 | Pass | The graph zoomed out without a problem. |
| Test 14 | Pass | The graph zoomed out without a problem. |
| Test 15 | Pass | The graph zoomed out without a problem. |
| Test 16 | Pass | I set the normalization factor to 0.001 and it zoomed out without a problem.
|
| Test 17 | Pass | I set the normalization factor to 0.001 and it zoomed out without a problem.
|
| Test 18 | Pass | I set the normalization factor to 0.001 and it zoomed out without a problem.
|
Web Service API Exploration
- The URLs to access in order to retrieve the desired data
- Any portions in these URLs that need to be substituted for specific queries, such as the gene name or ID within that web service
- You simply need to substitute the highlighted portion of the url with any specific yeast gene symbol in order to retrieve the .json data. https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=
BRO1.
- You simply need to substitute the highlighted portion of the url with any specific yeast gene symbol in order to retrieve the .json data. https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=
- Specific instructions on how to interpret the data returned by each URL so that you can extract exactly the information you need in order to proceed to the next step
- If you copy the URL that is used to access the desired data and hit enter, your computer will download a .json file that can be easily read in a text editor. From here, it is easy to read the data that is provided. You can also use the computer's terminal to invoke the
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1command in order to retrieve the data in a text form. This is a little bit more difficult to read but it is entirely possible to do so if you have some basic knowledge of reading .json. I however would recommend that an individual retrieving this data should use the method for downloading the .json file of the data so it is a bit easier to read.
- If you copy the URL that is used to access the desired data and hit enter, your computer will download a .json file that can be easily read in a text editor. From here, it is easy to read the data that is provided. You can also use the computer's terminal to invoke the
Electronic Notebook
- In order to complete the tests, I dowloaded the three files noted above onto my computer.
- In order to download the sif and graphml files, I needed to change the parameters from text files to all files.
- Once the files were on my desktop, all I had to do was follow the instructions for each test to complete them.
URL Explanation
- First, I used Dondi's hint to find the URL that retrieves json from our ajax-starter files.
- To get this, I inspected the loading box on bro1.html and hit the load button.
- I then clicked on the network tab on the inspection section and hovered my mouse over the
Gene?id=66043773in order to see the url. - By right-clicking on
Gene?id=66043773I was able to copy and paste the link. I then changedhttps://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773tohttps://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1in order to have the search parameters be in terms of the Gene's symbol. - Because this is on yeastmine, we didn't need to set a species parameter in the URL.
- Next I needed to simply type the
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1command into my command prompt to have it retrieve the json data. - I found that I can type the
https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1into a browser and download the data in .json format. - By opening the download in a text editor, it easily provides the data for a specific gene.
- I found that I can use any gene symbol to find the data for any specific gene simply by using the
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=template. - After my groups lifeline was used, we were told to focus on the primary identifier. In order to "filter" the data, we used the grep command:
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 | grep '"primaryIdentifier":"S'. - While using this command I found that when using the curl command in the terminal, we got the one data object we needed.
Acknowledgments
- John Lopez, Dina Bashoura, Simon Wroblewski and I worked together in the lab in order to complete the deliverables of this assignment. John Lopez and I worked together in person more than once to complete the deiverables of this assignment.
- John David N. Dionisio helped explain the use of curl to complete the deliverables of this assignment.
- While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.Hhinsch (talk) 23:32, 30 October 2017 (PDT)
References
- LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9.
- BRO1 HTML File. (2017). Retrieved October 30,2017, from BRO1 HTML File.
- GRNsight Client Side Testing Document: Normalization + Zoom. (2017). Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/images/9/9d/GRNsight_Testing-Normalization_and_Zoom.pdf.
- GRNsight. (2017) Retrieved October 29, 2017, from http://dondi.github.io/GRNsight/.
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