Cwong34 Week 9

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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."
  • To specify the taxon ID for our strain of S. cerevisiae, we inspected the web browser, to see what they called the field where we enter the ID, which they called "taxon."

Curling ID

  • Using the information we gathered on the abbreviations for the specific fields we needed, we were able to come up with a URL for the search: http://www.uniprot.org/uploadlists/?from=GENENAME&to=ACC&format=tab&taxon=559292&query= and inserting the gene name after the "query=".
  • After curling this, we get the gene's information, including its ID, so we can isolate this and plug it in to for the Gene ID in uniprot.org/uniprot/ "Gene ID" .xml
  • We looked up how to replace everything that shows up with only the gene ID, using REGEX, and got grep $1 | sed "s/$1[[:space:]]*\([A-Za-z0-9]*\).*/\1/g")

Curling gene's data profile

  • We set the curl to "gene_id_, and inserted it into another curl, so we can get the specific gene's data profile.

Bash function

  • We made it a bash function, so you can run the command, ./getInfoForGene and enter the gene's name after, which will replace "$1" with the desired gene, giving its data profile.

Final code

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"

Acknowledgmenets

  1. I met with Eddie Azinge, and we worked on our testing of GRNsight and UniProt API exploration together.
  2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Cwong34 (talk) 17:15, 28 October 2017 (PDT)

References

  1. LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
  2. REGEX. (2017). Regular Expressions. Retrieved October 28, 2018, from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

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Shared Journals:

Group Project

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