*The Find function was used in Excel (via control + F) and the value '''#N/A''' was searched for ("Look In:" was set to Values). 6 instances of '''#N/A''' were found, which coheres with the difference of 6 that was found between the Match utility results and those of PSQL.

**The discrepant IDs are: bca199f, bca5253f, bca636c, bcad837b, bcal0235a, and bcal0239a

*bca199f, bca5253f, bca636c, and bcad837b were found to be a part of a sequence of letters and numbers under the label of "checksum"; these appeared to have been accidentally captured by the utilized Match command.

*bcal0235a and bcal0239a follow the previous identified gene name patterns, however, they both show up as database reference IDs (database reference to STRING, which is a database of known and predicted protein interactions; these data will be ignored as they do not fall under an entry that refers to a gene name.

**At this point, it was also realized that the commands utilized for Match and PSQL could use some adjustments with respect to the desired pattern. <code>p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]</code> was modified to <code>p?BCA[L,M,S]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]</code>; this new pattern was tested with XMLPipe DB match using the command <code>java -jar xmlpipedb-match-1.1.1.jar "p?BCA[L,M,S]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?" < filename.xml</code>. The new pattern resulted in 7126 matches which eliminates one discrepant and incorrect match.

==Export of Build 2, a custom version of GenMAPP builder: conducted on 12/1==

*Anu provided a [[Media:gmbuilder-genialomics-12012015-build-2.zip|custom build of GenMAPP builder]] that included a customized species profile for J2315 as the only change.

===Creating the database "B.cenocepacia_J2315_20151201_BUILD2_genialomics" in PostgreSQL===

*Steps taken were sourced from the [[Running GenMAPP Builder | 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, B.cenocepacia_J2315_20151201_gmbuilder-genialomics-20151201, 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-genialomics-12012015-build-2''' 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

===Data Import into ''gmbuilder-genialomics-12012015-build-2''===

*gmbuilder.bat in the gmbuilder-genialomics-12012015-build-2 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 ''gmbuilder-genialomics-12012015-build-2'', Username was set to postgres, Password was set to the password of the PostgreSQL database that was recently created. OK was clicked.

*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 (''B. cenocepacia J2315'')

*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). The database was given the name "Bc-Std_GEN_BL12_20151201.gdb".

===Database Testing Report for Build 2===

*[[GÉNialOMICS Gene Database Testing Report (Build 2 Export)|Testing Report for Build 2 Export]]

==Exports of Build 3 and 4, custom versions of GenMAPP builder: conducted on 12/3==

*Gene database (.gdb) exports were conducted for builds 3 and 4 of the customized GenMAPP builder.

*Build 3 of GenMAPP Builder: program was modified so that the gene names will be picked up from ORF data rather than ordered locus data.

*Build 4 of GenMAPP Builder: TallyEngine code was cleaned up and code errors were fixed.

===Creating the postgres databases for builds 3 and 4 of customized GenMAPP builder===

*pgAdmin III was launched and a connection to the server was made. "Databases" was right clicked and select "New Database..." was chosen. The database, for Build 3, was given the name ''B.cenocepacia_J2315_20151203_BUILD3_genialomics'', and OK was clicked. The same procedure was repeated for Build 4; the build 4 database was given the name ''B.cenocepacia_J2315_20151204_BUILD4_genialomics''.

*The new databases were selected and the Query Tool was launched. Open File was clicked in the Query Tool and ''gmbuilder.sql'' in the ''sql'' folder of the '''gmbuilder folder''' of Build 3 and Build 4 of the customized GenMAPP builder 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 databases with all of its tables. In order to ensure that the query properly worked, it was checked that 167 tables existed in the databases.

===Data Import into ''B.cenocepacia_J2315_20151203_BUILD3_genialomics'' and ''B.cenocepacia_J2315_20151204_BUILD4_genialomics''===

*gmbuilder.bat was launched in the respective GenMAPP builder folder for both of the exports involving the two custom builds.

*Under file -> configure database, the host was left as localhost, the port number was left as 5432, database name was set to ''B.cenocepacia_J2315_20151203_BUILD3_genialomics'', in the case of the third build of GenMAPP builder. The database name was set to ''B.cenocepacia_J2315_20151204_BUILD4_genialomics'' in the case of the fourth build.

*The username was set to postgres, Password was set to the password of the PostgreSQL server that was being utilized. OK was clicked.

*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 (''B. cenocepacia J2315'')

===Database Testing Report for Builds 3 and 4===

*[[GÉNialOMICS Gene Database Testing Report (Build 3 Export)|Testing Report for Build 3 Export]]

*[[GÉNialOMICS Gene Database Testing Report (Build 4 Export)|Testing Report for Build 4 Export]]

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