Difference between revisions of "Cazinge Week 9"

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(→‎Part 1: GRNsight Testing: proper formatting)
(→‎Acknowledgements: adding signiture)
 
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:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
 
:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
 
; Test 2
 
; Test 2
 
: Instructions:
 
: Instructions:
Line 23: Line 23:
 
:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
 
:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully lay out the mentioned network graph as specified from the SIF file.
 
; Test 3
 
; Test 3
 
: Instructions:
 
: Instructions:
Line 30: Line 30:
 
:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
 
:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully lay out the mentioned network graph as specified from the GraphML file.
 
; Test 4
 
; Test 4
 
: Instructions:
 
: Instructions:
Line 39: Line 39:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the left when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 
; Test 5
 
; Test 5
 
: Instructions:
 
: Instructions:
Line 48: Line 48:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the left when the SIF file is loaded and restrict graph to viewport is unchecked.
 
; Test 6
 
; Test 6
 
: Instructions:
 
: Instructions:
Line 57: Line 57:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the left when the GraphML file is loaded and restrict graph to viewport is unchecked.
 
; Test 7
 
; Test 7
 
: Instructions:
 
: Instructions:
Line 66: Line 66:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the right when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 
; Test 8
 
; Test 8
 
: Instructions:
 
: Instructions:
Line 75: Line 75:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the right when the SIF file is loaded and restrict graph to viewport is unchecked.
 
; Test 9
 
; Test 9
 
: Instructions:
 
: Instructions:
Line 84: Line 84:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the right when the GraphML file is loaded and restrict graph to viewport is unchecked.
 
; Test 10
 
; Test 10
 
: Instructions:
 
: Instructions:
Line 93: Line 93:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift down when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 
; Test 11
 
; Test 11
 
: Instructions:
 
: Instructions:
Line 102: Line 102:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift down when the SIF file is loaded and restrict graph to viewport is unchecked.
 
; Test 12
 
; Test 12
 
: Instructions:
 
: Instructions:
Line 111: Line 111:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift down when the GraphML file is loaded and restrict graph to viewport is unchecked.
 
; Test 13
 
; Test 13
 
: Instructions:
 
: Instructions:
Line 120: Line 120:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift up when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 
; Test 14
 
; Test 14
 
: Instructions:
 
: Instructions:
Line 129: Line 129:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift up when the SIF file is loaded and restrict graph to viewport is unchecked.
 
; Test 15
 
; Test 15
 
: Instructions:
 
: Instructions:
Line 138: Line 138:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift up when the GraphML file is loaded and restrict graph to viewport is unchecked.
 
; Test 16
 
; Test 16
 
: Instructions:
 
: Instructions:
Line 147: Line 147:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the center of the bounding box when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 
; Test 17
 
; Test 17
 
: Instructions:
 
: Instructions:
Line 156: Line 156:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*  
+
:* GRNsight appears to successfully shift to the center of the bounding box when the SIF file is loaded and restrict graph to viewport is unchecked.
 
; Test 18
 
; Test 18
 
: Instructions:
 
: Instructions:
Line 165: Line 165:
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 
: '''Conclusions:'''
 
: '''Conclusions:'''
−
:*
+
:* GRNsight appears to successfully shift to the center of the bounding box when the GraphML file is loaded and restrict graph to viewport is unchecked.
  
 
==Part 2: Web Service Exploration==
 
==Part 2: Web Service Exploration==
 +
===== UniProt =====
 +
* Relevant documentation:
 +
** http://www.uniprot.org/help/api
 +
** http://www.uniprot.org/help/api_idmapping
 +
** http://www.uniprot.org/help/api_retrieve_entries
 +
* Supplementary websites:
 +
** [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] web page
 +
* Technical information:
 +
** You will encounter ''redirects'' in these web services; web browsers handle this automatically, but if using '''curl''' make sure to add the '''-L''' switch (i.e., '''curl -L '''…)
 +
** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
 +
** UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
 +
* Miscellaneous information:
 +
** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''
 +
 +
===== Solution =====
 +
 +
;This is a bash function that we made to display the results from today's exercise:
 +
# '''NOTE:''' We are assuming that you are using bash for the purposes of running this command.
 +
# put this code into a file named getInfoForGene
 +
# run chmod +x ./getInfoForGene
 +
# use the function like so: ./getInfoForGene "GENE_NAME"
 +
#* ex: ./getInfoForGene PBS2
 +
 +
<pre>#!/bin/bash
 +
 +
gene_id=$(curl -L "http://www.uniprot.org/uploadlists/?from=GENENAME&to=ACC&format=tab&taxon=559292&query=$1" | grep $1 | sed "s/$1[[:space:]]*\([A-Za-z0-9]*\).*/\1/g")
 +
 +
curl -L "http://uniprot.org/uniprot/$gene_id.xml"</pre>
 +
 +
===== Notebook =====
 +
 +
When doing this assignment, we first made a point of identifying and outlining the endpoints that we'd need to go from the gene name to the gene description; of which there were 2: turning the gene name into the matching uniprot id; then turning the uniprot id into the gene's information page. It was pretty clear how to do the latter part, which had been provided to us in an earlier assignment, but to do the former, we needed to use Uniprot's format conversion endpoint. First we found what parameters we'd need to provide to the endpoint, inspecting the elements to find the names of the specific parameters, and we promptly became stuck on the taxon id because our answers weren't being restricted solely to the genes that we wanted. Luckily, however, Dondi's notes provided us with the taxon id we needed, speeding up our process of getting to the answer. After we were able to get the uploadlists endpoint to work, we just needed to extract the id from the tab delimited output. we ran into a problem regarding POSIX-based whitespace, but we resolved it using the sed command you see provided. Finally, we assigned that output to a variable and fed it into the gene description endpoint.
 +
 +
==Links and References==
 +
 +
===Acknowledgements===
 +
 +
#Met outside of class with [[User:Cwong34|Corinne Wong]] to discuss any questions we had prior to meeting and throughout the process of completing the Week 9 assignment.
 +
 +
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 +
 +
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 15:44, 6 November 2017 (PST)
 +
 +
===References===
 +
 +
#LMU BioDB 2017. (2017). Week 9. Retrieved October 17, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
  
 
{{Template:Cazinge}}
 
{{Template:Cazinge}}

Latest revision as of 23:44, 6 November 2017

Part 1: GRNsight Testing

XLSX file

SIF file

GRAPHML file

GRNsight Client Side Testing Document: D-Pad Control

Last Updated: 2017-10-23

Test 1
Instructions:
  • Load Graph - File Menu -> Open
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
Conclusions:
  • GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
Test 2
Instructions:
  • Load Graph - File Menu -> Import SIF
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
Conclusions:
  • GRNsight appears to successfully lay out the mentioned network graph as specified from the SIF file.
Test 3
Instructions:
  • Load Graph - File Menu -> Import GraphML
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
Conclusions:
  • GRNsight appears to successfully lay out the mentioned network graph as specified from the GraphML file.
Test 4
Instructions:
  • Load Graph - File Menu -> Open
  • D-Pad Control - Click Right Arrow
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
Conclusions:
  • GRNsight appears to successfully shift to the left when the Excel workbook is loaded and restrict graph to viewport is unchecked.
Test 5
Instructions:
  • Load Graph - File Menu -> Import SIF
  • D-Pad Control - Click Right Arrow
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
Conclusions:
  • GRNsight appears to successfully shift to the left when the SIF file is loaded and restrict graph to viewport is unchecked.
Test 6
Instructions:
  • Load Graph - File Menu -> Import GraphML
  • D-Pad Control - Click Right Arrow
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
Conclusions:
  • GRNsight appears to successfully shift to the left when the GraphML file is loaded and restrict graph to viewport is unchecked.
Test 7
Instructions:
  • Load Graph - File Menu -> Open
  • D-Pad Control - Click Left Arrow
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
Conclusions:
  • GRNsight appears to successfully shift to the right when the Excel workbook is loaded and restrict graph to viewport is unchecked.
Test 8
Instructions:
  • Load Graph - File Menu -> Import SIF
  • D-Pad Control - Click Left Arrow
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
Conclusions:
  • GRNsight appears to successfully shift to the right when the SIF file is loaded and restrict graph to viewport is unchecked.
Test 9
Instructions:
  • Load Graph - File Menu -> Import GraphML
  • D-Pad Control - Click Left Arrow
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
Conclusions:
  • GRNsight appears to successfully shift to the right when the GraphML file is loaded and restrict graph to viewport is unchecked.
Test 10
Instructions:
  • Load Graph - File Menu -> Open
  • D-Pad Control - Click Up Arrow
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
Conclusions:
  • GRNsight appears to successfully shift down when the Excel workbook is loaded and restrict graph to viewport is unchecked.
Test 11
Instructions:
  • Load Graph - File Menu -> Import SIF
  • D-Pad Control - Click Up Arrow
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
Conclusions:
  • GRNsight appears to successfully shift down when the SIF file is loaded and restrict graph to viewport is unchecked.
Test 12
Instructions:
  • Load Graph - File Menu -> Import GraphML
  • D-Pad Control - Click Up Arrow
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
Conclusions:
  • GRNsight appears to successfully shift down when the GraphML file is loaded and restrict graph to viewport is unchecked.
Test 13
Instructions:
  • Load Graph - File Menu -> Open
  • D-Pad Control - Click Down Arrow
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
Conclusions:
  • GRNsight appears to successfully shift up when the Excel workbook is loaded and restrict graph to viewport is unchecked.
Test 14
Instructions:
  • Load Graph - File Menu -> Import SIF
  • D-Pad Control - Click Down Arrow
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
Conclusions:
  • GRNsight appears to successfully shift up when the SIF file is loaded and restrict graph to viewport is unchecked.
Test 15
Instructions:
  • Load Graph - File Menu -> Import GraphML
  • D-Pad Control - Click Down Arrow
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
Conclusions:
  • GRNsight appears to successfully shift up when the GraphML file is loaded and restrict graph to viewport is unchecked.
Test 16
Instructions:
  • Load Graph - File Menu -> Open
  • D-Pad Control - Click Center Button
Results:
  • GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
Conclusions:
  • GRNsight appears to successfully shift to the center of the bounding box when the Excel workbook is loaded and restrict graph to viewport is unchecked.
Test 17
Instructions:
  • Load Graph - File Menu -> Import SIF
  • D-Pad Control - Click Center Button
Results:
  • GRNsight should lay out a network graph from the SIF file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
Conclusions:
  • GRNsight appears to successfully shift to the center of the bounding box when the SIF file is loaded and restrict graph to viewport is unchecked.
Test 18
Instructions:
  • Load Graph - File Menu -> Import GraphML
  • D-Pad Control - Click Center Button
Results:
  • GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
  • if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
Conclusions:
  • GRNsight appears to successfully shift to the center of the bounding box when the GraphML file is loaded and restrict graph to viewport is unchecked.

Part 2: Web Service Exploration

UniProt
  • Relevant documentation:
  • Supplementary websites:
  • Technical information:
    • You will encounter redirects in these web services; web browsers handle this automatically, but if using curl make sure to add the -L switch (i.e., curl -L …)
    • 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')
    • UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
  • Miscellaneous information:
    • You will encounter the need for a taxon ID, which identifies a specific organism; the taxon ID for our strain of S. cerevisiae is 559292
Solution
This is a bash function that we made to display the results from today's exercise
  1. NOTE: We are assuming that you are using bash for the purposes of running this command.
  2. put this code into a file named getInfoForGene
  3. run chmod +x ./getInfoForGene
  4. use the function like so: ./getInfoForGene "GENE_NAME"
    • ex: ./getInfoForGene PBS2
#!/bin/bash

gene_id=$(curl -L "http://www.uniprot.org/uploadlists/?from=GENENAME&to=ACC&format=tab&taxon=559292&query=$1" | grep $1 | sed "s/$1[[:space:]]*\([A-Za-z0-9]*\).*/\1/g")

curl -L "http://uniprot.org/uniprot/$gene_id.xml"
Notebook

When doing this assignment, we first made a point of identifying and outlining the endpoints that we'd need to go from the gene name to the gene description; of which there were 2: turning the gene name into the matching uniprot id; then turning the uniprot id into the gene's information page. It was pretty clear how to do the latter part, which had been provided to us in an earlier assignment, but to do the former, we needed to use Uniprot's format conversion endpoint. First we found what parameters we'd need to provide to the endpoint, inspecting the elements to find the names of the specific parameters, and we promptly became stuck on the taxon id because our answers weren't being restricted solely to the genes that we wanted. Luckily, however, Dondi's notes provided us with the taxon id we needed, speeding up our process of getting to the answer. After we were able to get the uploadlists endpoint to work, we just needed to extract the id from the tab delimited output. we ran into a problem regarding POSIX-based whitespace, but we resolved it using the sed command you see provided. Finally, we assigned that output to a variable and fed it into the gene description endpoint.

Links and References

Acknowledgements

  1. Met outside of class with Corinne Wong to discuss any questions we had prior to meeting and throughout the process of completing the Week 9 assignment.

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

Cazinge (talk) 15:44, 6 November 2017 (PST)

References

  1. LMU BioDB 2017. (2017). Week 9. Retrieved October 17, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9

My Links

My User Page

My Electronic Notebook

Home Page

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