Gene Database Testing Report- cw20151201

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Files Asked for in the Gene Database Testing Report

For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: File:Gdtr cw20151201.zip

Pre-requisites

The following set of software was used in the creation and testing of the Bordetella pertussis 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\bpertussis_cw20151201 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 first custom version of gmbuilder including the Bordetella pertussis custom class: File:Dist cw20151201.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_cw20151201_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_cw20151201_gmb3build5custom
    • 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 selected "Bordetella pertussis (strain Tohama I/ATCC BAA-589/NCTC 13251), Taxon ID 257313" as the gene database species and then clicked Next.
  • The database was saved as bpertussis-std_cw20151201.
  • 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

Export Information

Version of GenMAPP Builder: Version 3.0.0 Build 5

Computer on which export was run: Seaver 120- Last computer on the right in the row farthest from the front of the room

Postgres Database name: bpertussis_cw20151201_gmb3build5custom

UniProt XML filename: File:Uniprot-proteome-UP000002676 cw20151201.zip

GO OBO-XML filename: File:Go daily-termdb cw20151201.zip

  • GO OBO-XML version (The version information was found in the file properties): Last Modified- ‎‎December ‎01, ‎2015, ‏‎2:21:31 AM
  • GO OBO-XML download link: Gene Ontology legacy download page
  • Time taken to import: 7.08 minutes
  • Time taken to process: 4.42 minutes
    • Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb (6.99 minutes and 4.48 minutes respectively). No interruptions occurred during these processes.

GOA filename: File:145.B pertussis ATCC BAA-589 cw20151201.zip

  • GOA version (found in the Last modified field on the FTP site): Last Modified- 11/10/15 1:39:00 PM
  • GOA download link: for Bordetella pertussis strain Tohama I
  • Time taken to import: 0.04 minutes
    • Note: The import time was equal to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151119.gdb. No interruptions occurred during this process.

Name of .gdb file: File:Bpertussis-std cw20151201.zip

  • Time taken to export:
    • Start time: 4:06 PM
    • End time: 5:00 PM
    • Elapsed time: 54 minutes

Note: No interruptions occurred during the export process.

Confirming that Changes to GenMAPP Builder Worked As Expected

  1. Systems Table Update
    • In creating the Bordetella pertussis custom class, changes were implemented to edit the OrderedLocusNames column in the exported .gdb file. Specifically, the species should be listed as Bordetella pertussis and a custom GeneDB link should be included in this row.
    • To verify that these changes were working as expected, I opened the file bpertussis-std_cw20151201.gdb in Microsoft Access. Upon opening Systems table here, all changes were successfully implemented:
      • Systemstable cw20151201.png
  2. GenMAPP Gene Backpage Update
    • The OrderedLocusNames GeneDB link added (as described above) also was designed to have funcitonality in GenMAPP. Sepcifically, gene backpages opened while using this gene database in GenMAPP should redirect users to the GeneDB information page for the specific Bordetella pertussis gene.
    • I specified bpertussis-std_cw20151201.gdb as the gene database in GenMAPP and put the gene BP3701 on the map. When I clicked on the link to the ID "BP3701" under "OrderedLocusNames" in Gene Finder, I was successfully brought to the corresponding GeneDB information page:
      • Custombackpage cw20151201.PNG

Team Information & Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein Week 11 Week 12 Week 14 Week 15
Lena Olufson Week 11 Week 12 Week 14 Week 15
Mahrad Saeedi Week 11 Week 12 Week 14 Week 15
Team Entries Week 11 Week 12 Week 14 Week 15

Group Members

Team Weekly Assignments

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
  • Week 11 (midnight 11/17)
  • Week 12 (midnight 11/24)
  • Week 14 (midnight 12/8)
  • Week 15 (midnight 12/15)
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