QLanners Week 9 - Revision history

Qlanners: fixed reference citation

2017-10-31T04:01:37Z

fixed reference citation

Qlanners: added link to dondi page

2017-10-31T04:00:31Z

added link to dondi page

Qlanners: added acknowledgement for Dr. Dahlquist

2017-10-31T03:59:51Z

added acknowledgement for Dr. Dahlquist

Qlanners: fixed links that were acting weird

2017-10-31T03:52:20Z

fixed links that were acting weird

Qlanners: added links

2017-10-30T20:04:57Z

added links

Qlanners: added quotations around certain links

2017-10-30T19:40:53Z

added quotations around certain links

Qlanners: added headers for acknowledgements and references

2017-10-30T19:38:04Z

added headers for acknowledgements and references

Qlanners: added to part 1 on gunsight testing

2017-10-30T19:31:44Z

added to part 1 on gunsight testing

Qlanners: added link to testing documentation

2017-10-30T19:22:42Z

added link to testing documentation

Qlanners: added signatur

2017-10-30T19:16:13Z

added signatur

@@ Line 109: / Line 109: @@
 ==References==
-LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1
+LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
 ==Links==
 {{Template:QLannersLinks}}

@@ Line 93: / Line 93: @@
 ==Acknowledgements==
 #I met with [[User:Bhamilton18|Blair]] and [[User:Emmatyrnauer|Emma]] on 10/30 outside of class to work on the API exploration portion of the assignment. I then followed up with [[User:Mbalducc|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.
-#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.
+#[[User:Dondi|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

@@ Line 104: / Line 104: @@
 #*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.''' <br>
 [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 12:16, 30 October 2017 (PDT)

@@ Line 72: / Line 72: @@
 ===Solution===
 Links needed in order: <br>
-#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)
+#<code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=<gene_name>[gene]+AND+Saccharomyces+cerevisiae[Organism]</nowiki></code> (where <gene_name> is replaced by the name of symbol of the desired gene)
-#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)
+#<code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<gene_id></nowiki></code> (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 began by using the general URL for all E-utility calls: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/</nowiki></code>
-**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 followed this up by adding esearch.fcgi?db=<database>&term=<query> to do a basic search. This gave us the URL: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query></nowiki></code>
 **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
+***We used the gene PBS2 to align with the results found in the ajax-starter package. This left us with the URL: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2</nowiki></code>
 ***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 left us with the URL: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2+AND+Saccharomyces+cerevisiae</nowiki></code> (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.
+**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: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]</nowiki></code> 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]
+**Thus we added the category [gene] after the gene name pbs2 and the category [organism] after the organism name, leaving us with the URL: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]</nowiki></code>
 ***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 returned ID number was then taken and replaced for <gene_id> in the following URL: <code><nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<gene_id></nowiki></code>
-**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.
+**This URL (<code>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=853313</code>) 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.

@@ Line 72: / Line 72: @@
 ===Solution===
 Links needed in order: <br>
-#"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)
+#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)
-#"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)
+#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.
@@ Line 109: / Line 109: @@
 ==References==
 LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1

@@ Line 7: / Line 7: @@
 '''Note:''' Both my partner [[User:Mbalducc|Mary]] and I used the same files for testing.
 <br>
 *Test 1
 **Passed
@@ Line 50: / Line 52: @@
 ==Part 2: Web Service API Exploration==
 *'''Goal:''' To take a gene name and find a path to its full data profile
 *'''Assigned database:''' NCBI
@@ Line 67: / Line 70: @@
 *** NCBI abbreviates the gene name/symbol field as ''sym''
 *** NCBI stores ''organism''s by their full name, in our case ''Saccharomyces cerevisiae'' (note the space)
-*'''Solution:'''
+===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/
@@ Line 77: / Line 84: @@
 ***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 liit the results.
+**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 <geneid> in the following URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=<geneid>
+**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 then returned a data profile for the gene PBS2.
+**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 trued this method for multiple gene names (ada2 and asp1) and recieved the same results. Confirming that this method works.
+**We tried this method for multiple gene names (ada2 and asp1) and got similar results. Confirming that this method works.
 ==Acknowledgements==

@@ Line 1: / Line 1: @@
-==Electronic Journal==
+==Part 1: GRNsight Client Side Testing Document: Edge Weights + Gray Threshold==
-===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 <br>
-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: <br>
 <br>
 *Test 1
@@ Line 42: / Line 46: @@
 *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. 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.
+**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.
-===Web Service API Exploration===
+==Part 2: Web Service API Exploration==
 *'''Goal:''' To take a gene name and find a path to its full data profile
 *'''Assigned database:''' NCBI