Bhamilton18 Week 9

Notebook

Hands-On with GRNsight

We worked on the Gray Threshold + Zoom portion of the GRNsight Beta version.

Test Files Found at: Gray Threshold + Zoom

1. Test 1 for file: 21-genes_31-edges_Schade-data_input.xlsx
   • Expected: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
   • Occurred: PASSED TEST
2. Test 2 for 21-genes_31-edges_Schade-data_estimation_output.sif
   • Expected: GRNsight should lay out a network graph from the SIF file if there are no errors in the file.
   • Occurred: PASSED TEST
3. Test 3 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
   • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file.
   • Occurred: PASSED TEST
4. Test 4 for 21-genes_31-edges_Schade-data_input.xlsx
   • Expected: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
   • Occurred: FAILED TEST This version for the xlsx file did not have a grey threshold option therefore the test could not be completed. Screenshot below.
     • 

       No Grey Threshold Option
5. Test 5 for 21-genes_31-edges_Schade-data_estimation_output.sif
   • Expected: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
   • Occurred: PASSED TEST
6. Test 6 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
   • Expected: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.
   • Occurred: FAILED TEST This version for the graphtml file did not have a grey threshold option therefore the test could not be completed. Screenshot below.
     • 

       No Grey Threshold Option
7. Test 7 for 21-genes_31-edges_Schade-data_input.xlsx
   • Expected:GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should zoom in (get larger).
   • Occurred: PASSED TEST
8. Test 8 for 21-genes_31-edges_Schade-data_estimation_output.sif
   • Expected:GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should zoom in (get larger).
   • Occurred: PASSED TEST
9. Test 9 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
   • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger).
   • Occurred: PASSED TEST
10. Test 10 for 21-genes_31-edges_Schade-data_input.xlsx
    • Expected:GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom in (get larger).
    • Occurred: FAILED TEST This is due to the earlier problem of no Grey Threshold option.
11. Test 11 for 21-genes_31-edges_Schade-data_estimation_output.sif
    • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger).
    • Occurred: PASSED TEST
12. Test 12 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
    • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger).
    • Occurred: FAILED TEST This is due to the earlier problem of no Grey Threshold option.
13. Test 13 for 21-genes_31-edges_Schade-data_input.xlsx
    • Expected: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should zoom out (get smaller).
    • Occurred: PASSED TEST
14. Test 14 for 21-genes_31-edges_Schade-data_estimation_output.sif
    • Expected: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should zoom out (get smaller).
    • Occurred: PASSED TEST
15. Test 15 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
    • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom out (get smaller).
    • Occurred: PASSED TEST
16. Test 16 for 21-genes_31-edges_Schade-data_input.xlsx
    • Expected: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray.The graph should zoom out (get smaller).
    • Occurred: FAILED TEST This is due to the earlier problem of no Grey Threshold option.
17. Test 17 for 21-genes_31-edges_Schade-data_estimation_output.sif
    • Expected: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller).
    • Occurred: PASSED TEST
18. Test 18 for 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
    • Expected: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller).
    • Occurred: FAILED TEST This is due to the earlier problem of no Grey Threshold option.

Attempted tests earlier in the day and received no results/displays for any file type. Later I reloaded the downloads of the Excel worksheet, sif and graphml files double checking their end tags and the tests began to pass.

Web Service API Exploration

NCBI Dondi Hints

• 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)

API NCBI Results

To begin, we looked at the Searching a Database website given to us by Dr. Dionisio. This allowed us to find the general search URl which as follows:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

This URL calls all utility calls for the database. Next, we added another portion to the URL to find the "gene" database, whcih was given to us by the website above. The URL should no look as follows:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>

For this portion we would change <database> to gene and <query> to any gene you want, some examples: asp1 or ada2.

Next, we looked at how other searches were formed within the database. For example if someone was looking for a scientific journal the form would look as follows in the URL science[journal]. Therefore for our URL we wanted gene specific data so we added a gene tag next to our gene. Example below:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=ada2[gene]

Lastly, we looked to find our gene specifically in the Saccharomyces cerevisiae organism. Therefore we had to add to our URL search an +AND+ function that specifies the Saccharomyces cerevisiae organism. since there is a space, we replace this with a + sign as noted above. Also, similar to the gene tag above we added a tag within the Saccharomyces cerevisiae to identify as [Organism]. The final result is below:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=ada2[gene]+AND+Saccharomyces+cerevisiae[Organism] 

Acknowledgments

1. I worked with my partner Emma Tyrnauer on this assignment.
2. Utilized this, (Gray Threshold + Zoom) document, in order to complete our detailed GRNsight beta testing.
3. We used three separate documents: Excel workbook (.xlsx), SIF (.sif) and GraphML (.graphml) files. These files were obtained from from this web page. The three different files that were chosen from the website were as follows:
   • 21-genes_31-edges_Schade-data_input.xlsx
   • 21-genes_31-edges_Schade-data_estimation_output.sif
   • 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml
4. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9

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