Blitvak Week 12

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