==Files Asked for in the Gene Database Testing Report==

==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: [[]]

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==

==Pre-requisites==

*I download the UniProt XML, GOA, and GO OBO-XML files for ''Bordetella Pertussis'' along with the GenMAPP Builder program.

*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.

**All files were saved to the folder ''Bklein7_CW\bpertussis_cw20151201'' 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.

====Downloaded GenMAPP Builder====

====Downloaded GenMAPP Builder====

# I downloaded the vanilla version of ''gmbuilder'' including the ''Bordetella pertussis'' custom class: [[File:Dist cw20151201.zip]].

# I downloaded the first custom version of ''gmbuilder'' including the ''Bordetella pertussis'' custom class: [[File:Dist cw20151201.zip]].

# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

# I extracted the GenMAPP Builder folder using [http://www.7-zip.org/ 7-zip].

* 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: ''bpertussis_cw20151201_gmb3build5custom''.

** 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 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.

* I typed my name in the owner field (Brandon Klein).

* 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''.

* 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_cw20151119''.

* 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.

* 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.

* Finally, I clicked the "Next" button to begin the export process.

Postgres Database name: bpertussis_cw20151201_gmb3build5custom

Postgres Database name: bpertussis_cw20151201_gmb3build5custom

UniProt XML filename: [[]]

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

* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11

* UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_11

* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]

* UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)]