GRNSight Edge Weight + Gray Threshold Test Results

Test 1

Passed
- The graph displayed.
- The edge weights showed only when I moused over them.

Test 2

Passed
- The graph displayed.
- The edge weights showed only when I moused over them.

Test 3

Passed
- The file opened and graph displayed.
- The edge weights showed only when I moused over them.

Test 4

Passed
- The graph displayed.
- The edge weights showed at all times.

Test 5

Passed
- The graph displayed.
- The edge weights showed at all times.

Test 6

Passed
- The graph displayed.
- The edge weights showed at all times.

Test 7

Passed
- The graph displayed.
- The edge weights never showed.

Test 8

Passed
- The graph displayed.
- The edge weights never showed.

Test 9

Passed
- The graph displayed.
- The edge weights never showed.

Test 10

Passed
- The graph displayed.
- The edge weights showed only when moused over.
- The lines turned gray at the new thresholds I set.

Test 11

Passed
- The graph displayed.
- The edge weights showed only when moused over.
- The lines turned gray at the new thresholds I set.

Test 12

Passed
- The graph displayed.
- The edge weights showed only when moused over.
- The lines turned gray at the new thresholds I set.

Test 13

Passed
- The graph displayed.
- The edge weights showed at all times.
- The lines turned gray at the new thresholds I set.

Test 14

Passed
- The graph displayed.
- The edge weights showed at all times.
- The lines turned gray at the new thresholds I set.

Test 15

Passed
- The graph displayed.
- The edge weights showed at all times.
- The lines turned gray at the new thresholds I set.

Test 16

Passed
- The graph displayed.
- The edge weights never showed.
- The lines turned gray at the new thresholds I set.

Test 17

Passed
- The graph displayed.
- The edge weights never showed.
- The lines turned gray at the new thresholds I set.

Test 18

Passed
- The graph displayed.
- The edge weights never showed.
- The lines turned gray at the new thresholds I set.

Web Service API Exploration

We were assigned the database NCBI Gene, which uses the data format XML.
The first link we used was to go from the gene name to the gene ID. This was: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=<gene_name>[gene]+AND+Saccharomyces+cerevisiae[Organism]
- <gene_name> is the name of the gene
Once we found the gene ID, we plugged it into this URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<gene_id>
- <gene_id> is the ID found from the first search
This process results in the XML data for that specific gene only.

Notes

GRNSight Tests:

I used the 21-genes_31-edges_Schade-data_estimation_output.graphml, 21-genes_31-edges_Schade-data_estimation_output.sif, and 21-genes_31-edges_Schade-data_estimation_output.xlsx files for the tests.
My partner used the same files as me so that we could confirm our results
I checked with my partner to make sure that he got the same results for each test as I did.

API Exploration:

We started by using this Searching a Database page
We used the general search link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>
- The <database> we were looking in was gene.
- The <query> is whatever gene you are looking for.
The example we used first was https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2
- This gave 539 results, so we had to narrow this down to genes contained within one organism, Saccharomyces cerevisiae.
To narrow down, we added the organism name, Saccharomyces cerevisiae to the term field, so that the URL became: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2+AND+Saccharomyces+cerivisiae
- This did narrow the results to 492, but did not get us what we wanted.
We searched the Searching a Database page again and found that adding bracketed categories to the terms would give us the results we wanted, so the next URL we tried was: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]
- This gave only one result, with the ID for PBS2 in Saccharomyces cerevisiae, which was 853313.
We then tried this again replacing the "pbs2" term with other genes.
- This worked to give their IDs as well.
The final step was to take the gene ID from that result page and use it to link to the page for that gene, we used the NCBI URL found in the ajax starter files to do this.
- We used this link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&id=<query>
  - The <query> is the gene ID
For PBS2, the link from the ID result page is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&id=853313

Acknowledgements

I worked with my homework partner, Quinn Lanners, on this assignment. We were not able to meet in person, but we did communicate over text to make sure we got the same results. For the Web API Exploration, we used the same genes as examples to make sure we both were using the same URLs and that they worked for both of us.

While I worked with the people noted above, this individual entry was completed by me and not copied from another source.

Mbalducc (talk) 16:36, 29 October 2017 (PDT)