Blitvak Week 12

• J2315
• TAXON ID: 623
• UP000001006

B.cenocepacia_J2315_20151119_gmb3build5

312777.B_cepacia.goa

Initial Export/Import Cycle

Initial Preparations

• Utilized the Week 9 Assignment as a reference

In preparation for this assignment, it was ensured that these programs were installed on a Windows workstation:

• 7-zip for the unpacking of compressed files
• PostgreSQL
• GenMAPP Builder
• Java JDK 1.8 64-bit (download jdk-8u65-windows-x64.exe)
• GenMAPP 2 (download GenMAPPv2Setup.exe)
• XMLPipeDB match utility
• A program that is able to read .mdb files (such as Microsoft Access)

Downloading the Required Files

Retrieving the UniProt XML file, Performed on 11/19

• The UniProt Complete Proteomes page was entered
• The Superkingdom Bacteria was selected as a Filter By option
• "burkholderia cenocepacia J2315" was added to the search bar and search was clicked upon. One result was given that corresponded to J2315.
• The result was clicked upon and, on the result page, UniProtKB was clicked upon in the "Map to" section (on left of the page)
• On the UniProtKB results page, Download was clicked; in the box that appeared, download all was selected, the format was set to XML, and the file was set to be compressed.
  • Referencing the entry name that corresponds to J2315, it was noticed that J2315 is also known as: ATCC BAA-245, DSM 16553, LMG 16656, NCTC 13227, and CF5610

Retrieving the GOA file, Performed on 11/19

• The UniProt-GOA ftp site was entered
• The link to the "proteomes" directory was clicked in the main directory
• In "proteomes", the GOA corresponding to the J2315 strain was not found.
• The GO annotations were found using the EMBL Quick GO browser: [[1]]

Retrieving the GO OBO-XML file, Performed on 11/19

• The GO OBO-XML file was downloaded from the Gene Ontology download page
• "obo-xml.gz" was selected/clicked under Legacy Downloads

Downloading/Updating GenMAPP Builder, Performed on 10/27

• The files were downloaded from the XMLPipeDB releases page on GitHub
• Download link for gmbuilder-3.0.0-build-5 (the version used in this assignment)
  • All of the downloaded files, if compressed, were extracted using 7-Zip. All required files were placed in one folder
• Downloaded on 10/27, Summary
  • The complete proteome for V. cholerae was downloaded from UniProtKB in the XML format
  • The GOA file for V. cholerae was downloaded from this link
  • The GO OBO-XML formatted file for V. cholerae was downloaded from the GO website
  • The most recent version (3.0.0, build 5) of gmBuilder was downloaded from GitHub

Export Process

Creating a New Database in PostgreSQL

• Steps taken were sourced from the Running GenMAPP Builder page
• pgAdmin III was launched and a connection to the server was made. "Databases" was right clicked and select "New Database..." was chosen. The database was given a name, V.cholerae_20151027_gmb3build5, and OK was clicked.
• The new database was selected and the Query Tool was launched. Open File was clicked in the Query Tool and gmbuilder.sql in the gmbuilder-3.0.0-build-5 folder (within the sql folder) was selected. Upon selection of that file, a query was loaded into Query Tool and it was subsequently executed by clicking the green "Execute Query" arrow
• This query populates the created database with all of its tables. In order to ensure that the query properly worked, it was checked that 167 tables existed in the database

Importing Data

• gmbuilder.bat in the gmbuilder folder was launched
• Under file -> configure database, the host was left as localhost, the port number was left as 5432, database name was set to V.cholerae_20151027_gmb3build5, Username was set to BL, Password was set to the password of the PostgreSQL database that was recently created. OK was clicked.

Data Import into V.cholerae_20151027_gmb3build5

• File -> Import UniProt XML was selected
  • The UniProt XML file that was previously extracted was chosen, open was clicked. The import process was allowed to proceed uninterrupted.
• File -> Import GO OBO-XML was selected
  • The GO OBO-XML that was previously extracted was chosen, open was clicked. The import process was allowed to proceed uninterrupted.
• File -> Import GOA was selected
  • The GOA file that was downloaded previously was chosen, open was clicked, and the import process was allowed to proceed uninterrupted.

Exporting a GenMAPP Gene Database (.gdb file)

• File -> Export to GenMAPP Gene Database was selected
• BL was typed into the Owner field. The species of interest was selected for export (V. cholerae)
• Next was clicked, the create GenMAPP database file/location was selected, and the boxes for the exporting of Molecular Function, Cellular Component, and Biological Process Gene Ontology Terms were left checked. The export process was initialized by clicking next; the windows were left open for the program to continue and finish with the export process (was estimated to take somewhere between 1-2 hrs).