Difference between revisions of "Bklein7 Week 12"

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(updated import process)
(updated database creation)
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* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
 
* I launched ''pgAdmin III'' and connected to the PostgreSQL 9.4 server (localhost:5432).
−
** On this server, I created a new database: ''V.cholerae_20151027_gmb3build5''.
+
** On this server, I created a new database: ''bpertussis_cw20151119_gmb3build5''.
 
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
 
** I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
 
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
 
*** I clicked on the Open File icon and selected the file ''gmbuilder.sql''. This imported a series of SQL commands into the editor tab.
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** Host or address: localhost
 
** Host or address: localhost
 
** Port number: 5432
 
** Port number: 5432
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** Database name: V.cholerae_20151027_gmb3build5
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** Database name: bpertussis_cw20151119_gmb3build5
 
** Username: postgres
 
** Username: postgres
 
** Password: Welcome1
 
** Password: Welcome1
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===Importing Data into the PostgreSQL Database===
 
===Importing Data into the PostgreSQL Database===
  
−
*The downloaded data files for ''Vibrio cholerea'' were specified and imported into the database by clicking on the following buttons:
+
*The downloaded data files for ''Bordetella pertussis'' were specified and imported into the database by clicking on the following buttons:
 
** Selected File > Import UniProt XML...
 
** Selected File > Import UniProt XML...
 
** Selected File > Import GO OBO-XML...
 
** Selected File > Import GO OBO-XML...

Revision as of 23:33, 19 November 2015

Files Asked for in the Gene Database Testing Report

For convenience, all of the files explicitly asked for in the "Gene Database Testing Report" section were compressed together in this file: File:Bklein7 Week9 Files.zip.

Pre-requisites

The following set of software was used in the creation and testing of the Vibrio cholerae gene database:

  1. 7-ziptool that for unpacking .gz and .zip files
  2. PostgreSQL on Windows (version 9.4.x)
  3. GenMAPP Builder
  4. Java JDK 1.8 64-bit
  5. GenMAPP 2
  6. XMLPipeDB match utility for counting IDs in XML files
  7. Microsoft Access for reading .mdb files

Gene Database Creation

Downloading Data Source Files and GenMAPP Builder

  • I download the UniProt XML, GOA, and GO OBO-XML files for Bordetella Pertussis along with the GenMAPP Builder program.
    • All files were saved to the folder Bklein7_CW on my computer's ThawSpace.
    • Files that required extraction were unzipped using 7-zip.
    • Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.

UniProt XML

GOA

GO OBO-XML

Downloaded GenMAPP Builder

  1. I downloaded the GenMAPP Builder zip folder: Download gmbuilder-3.0.0-build-5.zip.
  2. I extracted the GenMAPP Builder folder using 7-zip.

Creating the New Database in PostgreSQL

  • I launched pgAdmin III and connected to the PostgreSQL 9.4 server (localhost:5432).
    • On this server, I created a new database: bpertussis_cw20151119_gmb3build5.
    • I opened the SQL Editor tab to use an XMLPipeDB query to create the tables in the database.
      • I clicked on the Open File icon and selected the file gmbuilder.sql. This imported a series of SQL commands into the editor tab.
      • I clicked on the Execute Query icon to run this command.
      • In viewing the schema for this database, I confirmed that there were 167 tables after running the above command.

Configuring GenMAPP Builder to Connect to the PostgreSQL Database

  • To begin, I launched gmbuilder.bat.
  • I selected the "Configure Database" option and entered the following information into the fields below:
    • Host or address: localhost
    • Port number: 5432
    • Database name: bpertussis_cw20151119_gmb3build5
    • Username: postgres
    • Password: Welcome1

Importing Data into the PostgreSQL Database

  • The downloaded data files for Bordetella pertussis were specified and imported into the database by clicking on the following buttons:
    • Selected File > Import UniProt XML...
    • Selected File > Import GO OBO-XML...
    • Clicked OK to the message asking to process the GO data.
    • Selected File > Import GOA...

Exporting a GenMAPP Gene Database (.gdb)

  • I selected File > Export to GenMAPP Gene Database... to begin the export process.
  • I typed my name in the owner field (Brandon Klein).
  • I selectedVibrio cholerae as the gene database species and then clicked Next.
  • The database was saved as Vc-Std_BK_20151027.
  • I checked the boxes for exporting all Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms.
  • Finally, I clicked the "Next" button to begin the export process.

Gene Database Testing Report

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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