Difference between revisions of "Cwong34 Week 9"

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==Research==
 
==Research==
−
We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
+
*We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
 +
*To specify "Gene name" and "UniProtKB," we looked at [http://www.uniprot.org/help/api_idmapping mapping database identifiers] to identify the abbreviations for the categories. "Gene name" is "GENENAME," and "UniProtKB" is "ACC."
  
 
=Acknowledgmenets=
 
=Acknowledgmenets=

Revision as of 22:47, 28 October 2017

GRNsight

XLSX file

SIF file

GRAPHML file

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: I loaded the xlsx file, and the graph appeared on the page with no problems.
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: I imported the SIF file to the page, and the map showed up with no problems.
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: I imported the GraphML file to the page, and the map showed up with no problems.
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: I opened the Excel workbook, clicked the right arrow, and it correctly moved to the right.
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: I imported the SIF file, clicked the right arrow, and the map correctly moved to the right.
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: I imported the GraphML file, clicked the right arrow, and the map correctly moved to the right.
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: I opened the Excel workbook, clicked the left arrow, and the the map correctly moved to the left.
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: I imported the SIF file, clicked the left arrow, and the map correctly moved to the left.
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: I imported the GraphML file, clicked the left arrow, and the map correctly moved to the left.
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: I opened the Excel workbook, clicked the up arrow, and the map correctly moved up.
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: I imported the SIF file, clicked the up arrow, and the file correctly moved up.
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: I imported the GraphML file, clicked the up arrow, and the map correctly moved up.
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: I opened the Excel workbook, clicked the down arrow, and the map correctly moved down.
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: I imported the SIF file, clicked the down arrow, and the map correctly moved down.
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: I imported the GraphML file, clicked the down arrow, and the map correctly moved down.
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: I opened the Excel workbook, clicked the center button, and the map correctly moved to the center.
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: I imported the SIF file, clicked the center button, and the map correctly moved to the center.
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: I imported the GraphML file, clicked the center button, and the map correctly moved to the center.

API Exploration

UniProt

Research

  • We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the Retrieve/ID mapping link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of S. cerevisiae, which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
  • To specify "Gene name" and "UniProtKB," we looked at mapping database identifiers to identify the abbreviations for the categories. "Gene name" is "GENENAME," and "UniProtKB" is "ACC."

Acknowledgmenets

References

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

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