QLanners Week 9

Part 1: GRNsight Client Side Testing Document: Edge Weights + Gray Threshold

Link to testing documentation: https://xmlpipedb.cs.lmu.edu/biodb/fall2017/images/5/5f/GRNsight_Testing-Edge_Weights_and_Gray_Threshold.pdf
Links to files to be used for testing:

• https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.graphml (used for all tests involving a graphml file)
• https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.sif (used for all tests involving a sif file)
• https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx (used for all tests involving an Excel file)

Note: Both my partner Mary and I used the same files for testing.

Testing Results

All tests refer to the corresponding test in the testing documentation file provided above.

• Test 1
  • Passed
• Test 2
  • Passed
• Test 3
  • Passed
• Test 4
  • Passed
• Test 5
  • Passed
• Test 6
  • Passed
• Test 7
  • Passed
• Test 8
  • Passed
• Test 9
  • Passed
• Test 10
  • Passed
• Test 11
  • Passed
• Test 12
  • Passed
• Test 13
  • Passed
• Test 14
  • Passed
• Test 15
  • Passed
• Test 16
  • Passed
• Test 17
  • Passed
• Test 18
  • Passed

• Other Notes:
  • Every time you change the "Gray Edge Threshold" the Zoom level of the viewport resets itself. This makes it difficult to use the gray edge threshold, as you lose track of the genes you were paying attention to if you were zoomed in or out.
  • The first time I tried to load SIF and GRAPHML files on 10/24, the program would allow me to select my file, but nothing would load into the viewport. However, when I tried again on 10/26 both file types were loaded normally. Not sure if this was an issue with my local computer or the application itself. This error took place on both Safari and Chrome the first time I tried but worked on both browsers the second try.
    • Update: After talking to Blair on 10/30/17, it appears as though she experienced a similar problem. Although, she also had difficulty loading Excel files initially as well. Like my scenario, her issue was also resolved by simply trying agan at a later time.

Part 2: Web Service API Exploration

Background Information

• Goal: To take a gene name and find a path to its full data profile
• Assigned database: NCBI
• Dondi References:
  • Relevant documentation:
    • https://www.ncbi.nlm.nih.gov/gene
    • https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
  • Technical information:
    • Your URLs will include ampersands (&), which will need special handling with curl: in these cases, enclose the URL in apostrophes (e.g., curl -L 'http://www.uniport.org?query=this&type=that')
    • Your URLs will also include brackets ([ ]), which will need special handling with curl: in these cases, make sure to add the -g switch (i.e., curl -g …)
    • Your URLs may include spaces; typically, we replace those with + (plus) symbols
  • Miscellaneous information:
    • NCBI consists of multiple databases; we care about the gene database
    • NCBI abbreviates the gene name/symbol field as sym
    • NCBI stores organisms by their full name, in our case Saccharomyces cerevisiae (note the space)

Solution

Links needed in order:

1. "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=<gene_name>[gene]+AND+Saccharomyces+cerevisiae[Organism]" (where <gene_name> is replaced by the name of symbol of the desired gene)
2. "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<gene_id>" (where <gene_id> is replaced by the gene ID retrieved from the first URL)

Process to arrive at solution

• • We primarily worked with the https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database web page to find this path.
  • We began by using the general URL for all E-utility calls: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
  • We followed this up by adding esearch.fcgi?db=<database>&term=<query> to do a basic search. This gave us the URL: "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>"
  • We then replaced the <database> section of the URL with gene (per the miscellaneous information above) and substituted the <query> section with the name of a gene.
    • We used the gene PBS2 to align with the results found in the ajax-starter package. This left us with the URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2
    • This URL returned 539 results of different IDs in a list
  • From here we added Saccharomyces cerevisiae toour query to limit the results to this organism only.
    • This left us with the URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2+AND+Saccharomyces+cerevisiae (subsituting the spaces with +)
    • This returned 492 resuts of different IDs in a list.
  • Finally, looking once again at the web page https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database we saw the following example: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat] and hypothesized that if we added brackets indicating a category for both the terms in the query that it would limit the results.
  • Thus we added the category [gene] after the gene name pbs2 and the category [organism] after the organism name, leaving us with the URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]
    • This URL returned one result of an ID in a list.
  • This returned ID number was then taken and replaced for <gene_id> in the following URL: "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<gene_id>"
  • This URL (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=853313) then returned a data profile for the gene PBS2.
  • We tried this method for multiple gene names (ada2 and asp1) and got similar results. Confirming that this method works.

Acknowledgements

1. I met with Blair and Emma on 10/30 outside of class to work on the API exploration portion of the assignment. I then followed up with Mary (who was unable to make it to the meeting due to work) through text. We touched base on both the GRNsight testing and API exploration portion of the assignment to make sure we were on the same page.
2. Dr. Dondi for the in-class lectures on how to begin the API web service exploration journey, and for providing the following resources listed below to begin the process.
   • https://www.ncbi.nlm.nih.gov/gene
   • https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
   • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
   • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
   • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
3. The following files were utilized for GRnsight testing purposes from https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files
   • https://xmlpipedb.cs.lmu.edu/biodb/fall2017/images/5/5f/GRNsight_Testing-Edge_Weights_and_Gray_Threshold.pdf
   • 21-genes_31-edges_Schade-data_estimation_output.graphml for the graphml file tests
   • 21-genes_31-edges_Schade-data_estimation_output.sif for the sif file tests
   • 21-genes_31-edges_Schade-data_estimation_output.xlsx for the Excel file tests

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Qlanners (talk) 12:16, 30 October 2017 (PDT)

References

LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1