Difference between revisions of "Hhinsch Week 9"

Latest revision as of 06:54, 31 October 2017

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

Web Service API Exploration

• The URLs to access in order to retrieve the desired data
  • https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1
• 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.
• 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=BRO1 command 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 would like to obtain a sole object of the gene's data, you can use the curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 | grep '"primaryIdentifier":"S' command in the terminal, then copy the text to a code reader such as atom.
  • I however believe that simply using the https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 url in the browser to download a .json file of the data is the best option. This is because you can open the .json file in a code reader, and it contains additional identifiers that may be useful.

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=66043773 in order to see the url.
• By right-clicking on Gene?id=66043773 I was able to copy and paste the link. I then changed https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773 to https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 in 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=BRO1 command 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=BRO1 into 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

1. 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.
2. John David N. Dionisio helped explain the use of curl to complete the deliverables of this assignment.
3. 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

1. LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9.
2. BRO1 HTML File. (2017). Retrieved October 30,2017, from BRO1 HTML File.
3. 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.
4. GRNsight. (2017) Retrieved October 29, 2017, from http://dondi.github.io/GRNsight/.

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