Emmatyrnauer Week 9 - Revision history

Emmatyrnauer: /* References */ typo

2017-10-31T06:23:48Z

‎References: typo

Emmatyrnauer: /* Acknowledgements */ adding files

2017-10-31T06:22:52Z

‎Acknowledgements: adding files

Emmatyrnauer: /* Web service API exploration for NCBI */ adding details

2017-10-31T06:19:27Z

‎Web service API exploration for NCBI: adding details

Emmatyrnauer: /* Web service API exploration for NCBI */ typo

2017-10-31T06:11:49Z

‎Web service API exploration for NCBI: typo

Emmatyrnauer: /* Web service API exploration for NCBI */ adding details

2017-10-31T06:10:49Z

‎Web service API exploration for NCBI: adding details

Emmatyrnauer: /* Hands on with GRNsight */ typos

2017-10-31T06:06:32Z

‎Hands on with GRNsight: typos

Emmatyrnauer: /* Hands on with GRNsight */ phrase consistency

2017-10-31T06:04:47Z

‎Hands on with GRNsight: phrase consistency

Emmatyrnauer: /* Hands on with GRNsight */ fixing silly mistakes--consistency with error in gray threshold

2017-10-31T06:03:43Z

‎Hands on with GRNsight: fixing silly mistakes--consistency with error in gray threshold

Emmatyrnauer: /* Acknowledgements */ adding to acknowledgments

2017-10-31T01:08:50Z

‎Acknowledgements: adding to acknowledgments

Emmatyrnauer: /* References */ adding references

2017-10-31T01:06:02Z

‎References: adding references

@@ Line 122: / Line 122: @@
 ==References==
 #LMU BioDB 2017. (2017). Gray Threshold + Zoom. Retrieved October 30, 2017, from [[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf]]
-#LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9]
+#LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
 {{Emmatyrnauer}}

@@ Line 113: / Line 113: @@
 #Blair and I also met up in person with [[User:Qlanners|Quinn Lanners]] who also was assigned the NCBI database.
 #[[User:Dondi]] for helping walk through the process and basics of this assignment during class
-#21-genes_31-edges_Schade-data_input.xlsx used for beta version of GRNsight testing
+#Files [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files from this web page]
-#21-genes_31-edges_Schade-data_estimation_output.sif used for beta version of GRNsight testing
+#*21-genes_31-edges_Schade-data_input.xlsx used for beta version of GRNsight testing
-#21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml used for beta version of GRNsight testing
+#*21-genes_31-edges_Schade-data_estimation_output.sif used for beta version of GRNsight testing
 #While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 18:00, 30 October 2017 (PDT)

@@ Line 102: / Line 102: @@
 #<code>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/</code> was used because this service requires performing an E-utility call.
 #We replaced <code><database> </code> with <code>gene</code> and <code><query></code> with <code>ADA2</code> (a specific gene) in <code>esearch.fcgi?db=<database>&term=<query></code> and added this to the growing URL to narrow the results to the gene database and a specific gene from NCBI.
-#[gene] was added to narrow the results further to gene specific data.
+#[gene] was added to narrow the results further to gene specific data. This was determined through the performance of different specific searches in the database (ie. in a search for a scientific journal one would put <code>scientific[journal]</code> to indicate the category).
-#<code>+AND+Saccharomyces+20cerevisiae[Organism]</code> allowed us to reach the final product by specifying the organism (Saccharomyces cerevisiae) where <code>+</code> replaced the spaces and <code>[Organism]</code> indicated that organism data was wanted.
+#<code>+AND+Saccharomyces+cerevisiae[Organism]</code> allowed us to reach the final product by specifying the organism (Saccharomyces cerevisiae) where <code>+</code> replaced all the spaces and <code>[Organism]</code> indicated that organism data was wanted.
 # The URL was tested with other specific genes and it worked!
 '''Final URL'''
-  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=ada2[gene]+AND+Saccharomyces+20cerevisiae[Organism]
+  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=ada2[gene]+AND+Saccharomyces+cerevisiae[Organism]
 ==Acknowledgements==

@@ Line 99: / Line 99: @@
 '''Process'''
-#We referenced [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database|Searching a Database] from the Relevant Documentation section in the Week 9 assignment page as well as the hints Dondi provided for syntax.
+#We referenced [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] from the Relevant Documentation section in the Week 9 assignment page as well as the hints Dondi provided for syntax.
 #<code>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/</code> was used because this service requires performing an E-utility call.
 #We replaced <code><database> </code> with <code>gene</code> and <code><query></code> with <code>ADA2</code> (a specific gene) in <code>esearch.fcgi?db=<database>&term=<query></code> and added this to the growing URL to narrow the results to the gene database and a specific gene from NCBI.

@@ Line 97: / Line 97: @@
 ===Web service API exploration for NCBI===
 #We referenced [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database] from the Relevant Documentation section in the Week 9 assignment page.
 #<code>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/</code> was used because this service requires performing an E-utility call.
 #We replaced <code><database> </code> with <code>gene</code> and <code><query></code> with <code>ADA2</code> (a specific gene) in <code>esearch.fcgi?db=<database>&term=<query></code> and added this to the growing URL to narrow the results to the gene database and a specific gene from NCBI.
-#[gene] was added to narrow the results further to gene specific data
+#[gene] was added to narrow the results further to gene specific data.
 #<code>+AND+Saccharomyces+20cerevisiae[Organism]</code> allowed us to reach the final product by specifying the organism (Saccharomyces cerevisiae) where <code>+</code> replaced the spaces and <code>[Organism]</code> indicated that organism data was wanted.
 '''Final URL'''

@@ Line 21: / Line 21: @@
 *Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value
 *Expected results: 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
-*''Results: Failed; the zoom function was not visible''
+*''Results: Failed; gray threshold function not visible''
 [[File:Emmat_week9_xslx.png|400px|thumb|right| Test 4: Zoom function missing in bottom left corner of display for Excel workbook]]
@@ Line 32: / Line 32: @@
 *Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value
 *Expected results: 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
-*''Results: Failed; the zoom function was not visible''
+*''Results: Failed; gray threshold function not visible''
 [[File:Emmat_week9_graphml.png|400px|thumb|right| Test 6: Zoom function missing in bottom left corner of display for GraphML]]

@@ Line 53: / Line 53: @@
 *Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value Zoom Slider - Increase Zoom Level
 *Expected results: 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)
-*''Results: Passed''
+*''Results: Failed; gray threshold function not visible''
 '''Test 11'''
@@ Line 63: / Line 63: @@
 *Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Increase Zoom Level
 *Expected results: 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 in (get larger).
-*''Results: Passed''
+*''Results: Failed; gray threshold function not visible''
 '''Test 13'''
@@ Line 84: / Line 84: @@
 *Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
 *Expected results: 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)
-*''Results: Passed''
+*''Results: Failed; gray threshold function not visible''
 '''Test 17'''
@@ Line 94: / Line 94: @@
 *Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
 *Expected results: 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)
-*''Results: Passed''
+*''Results: Failed; gray threshold function not visible''
 ===Web service API exploration for NCBI===

← Older revision		Revision as of 01:06, 31 October 2017
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	==References==		==References==
		+	#LMU BioDB 2017. (2017). Gray Threshold + Zoom. Retrieved October 30, 2017, from [[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf]]
		+	#LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9]
		+
	{{Emmatyrnauer}}		{{Emmatyrnauer}}