Difference between revisions of "Bklein7 Week 12"

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(Created Page and copied over some info from week 9 for reference)
 
(updated import process)
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===Downloading Data Source Files and GenMAPP Builder===
 
===Downloading Data Source Files and GenMAPP Builder===
  
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*I download the UniProt XML, GOA, and GO OBO-XML files for ''Vibrio cholerae'' along with the GenMAPP Builder program.
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*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.
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**All files were saved to the folder ''Bklein7_Week9'' on my computer's ThawSpace.
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**All files were saved to the folder ''Bklein7_CW'' on my computer's ThawSpace.
 
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
 
**Files that required extraction were unzipped using [http://www.7-zip.org/ 7-zip].
 
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.
 
**Data files that remained in a folder after unzipping were removed from their folders to facilitate organization and command line processing.
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* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
 
* I went to the [http://www.uniprot.org/taxonomy/complete-proteomes UniProt Complete Proteomes] page.
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**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/uniprot/?query=organism:243277 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)].
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**From there, I navigated to the complete proteome download page for [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)].
 
** I clicked on the "Download" button at the top of the page above and selected the following options:
 
** I clicked on the "Download" button at the top of the page above and selected the following options:
 
***"Download all"
 
***"Download all"
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* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
 
* UniProt-GOA files can be downloaded from the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/ UniProt-GOA ftp site].
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*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/46.V_cholerae_ATCC_39315.goa GO annotations for ''Vibrio cholerae''].
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*Within the above site, I navigated to the [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I].
 
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.
 
**This text file was automatically opened by my browser. Therefore, I had to manually download the file.
  

Revision as of 23:19, 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: V.cholerae_20151027_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: V.cholerae_20151027_gmb3build5
    • Username: postgres
    • Password: Welcome1

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:
    • 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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