* Extract the UniProt XML and GO OBO-XML .gz files using [http://www.7-zip.org/ 7-zip] or other utility.

* Extract the UniProt XML and GO OBO-XML .gz files using [http://www.7-zip.org/ 7-zip] or other utility.

== Create New Database in PostgreSQL ==

== Create New Database in PostgreSQL ==

* Launch pgAdmin III.

* Launch pgAdmin III.

* Double-click on PostgreSQL 9.2 (localhost:5432) on the upper left hand side of the window.

* Double-click on PostgreSQL 9.4 (localhost:5432) on the upper left hand side of the window.

** This is the equivalent of connecting you to the server and you may be asked for a password at this point.

** This is the equivalent of connecting you to the server and you may be asked for a password at this point.

* Right click on "Databases" and Select "New Database..."

* Right click on "Databases" and Select "New Database..."

* Give the database a name in the "Name" field and click OK.

* Give the database a name in the "Name" field and click OK.

* Click on your new database name in the treeview on the left.

** Take some care in selecting a meaningful name.  It is good practice to at least include the species and today's date in the name.

* Double-left-click on your new database name in the treeview on the left.

* Click on the SQL icon in the toolbar at the top of the window.

* Click on the SQL icon in the toolbar at the top of the window.

** The SQL Editor tab will be open and there may be leftover query text in the upper pane.  Delete this text.  You are now going to use an XMLPipeDB query to create the tables in the database.

** The SQL Editor tab will be open and there may be leftover query text in the upper pane.  Delete this text.  You are now going to use an XMLPipeDB query to create the tables in the database.

* You should get a series of NOTICE messages in the Messages tab at the bottom of the window, concluding with a message like "Query returned successfully with no result in 15583 ms" in the end.  This query now created all the tables in the database (although there is still no data in them).

* You should get a series of NOTICE messages in the Messages tab at the bottom of the window, concluding with a message like "Query returned successfully with no result in 15583 ms" in the end.  This query now created all the tables in the database (although there is still no data in them).

* Close the query window (you don't need to save the query because you have already run it).

* Close the query window (you don't need to save the query because you have already run it).

* To double check that all is OK, click the + sign for the database, then the + sign for Schemas, then finally the + sign for public.  Under the Tables section, you should see a count of 159 in parentheses.

* To double check that all is OK, click the + sign for the database, then the + sign for Schemas, then finally the + sign for public.  Under the Tables section, you should see a count of 167 in parentheses.

== Configuring GenMAPP Builder to Connect to your PostgreSQL Database ==

== Configuring GenMAPP Builder to Connect to your PostgreSQL Database ==

* Launch gmbuilder.bat (or gmbuilder-32bit.bat)

* Launch gmbuilder.bat.

** If the program does not detect a database configuration, you will see a message window to this effect and the configuation dialog will open automatically once you close the message window.  Otherwise:

** If the program does not detect a database configuration, you will see a message window to this effect and the configuation dialog will open automatically once you close the message window.  Otherwise:

* Select the menu item File > Configure Database...

* Select the menu item File > Configure Database...

** Port number: 5432

** Port number: 5432

** Database name: <enter the name of the PostgreSQL database you created above>

** Database name: <enter the name of the PostgreSQL database you created above>

** Username: <enter the username of the PostgreSQL database you created above>

** Username: <enter the username of the PostgreSQL database you created above>; in S120, this username is "postgres"

** Password: <enter the password of the PostgreSQL database you created above>

** Password: <enter the password of the PostgreSQL database you created above>; in S120, ask the instructors for the password.

* Click the OK button.

* Click the OK button.

** Navigate to the UniProt XML file that you extracted previously and click the Open button.

** Navigate to the UniProt XML file that you extracted previously and click the Open button.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

* Select File > Import GO OBO-XML...

* Select File > Import GO OBO-XML...

** Navigate to the GO OBO-XML file that you extracted previously.  Click the Open button.

** Navigate to the GO OBO-XML file that you extracted previously.  Click the Open button.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

* Click OK to the message asking you to process the GO data.

**6.88 min

Click OK to the message asking you to process the GO data.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

** This should take about 5-10 minutes, but may take longer depending on the size of the file, processor speed, and available memory of the machine.  When the process has completed, record the elapsed time from the message window that appears.

* Select File > Import GOA...

* Select File > Import GOA...

** Navigate to the GOA file that you downloaded previously and click the Import button.  This process should only take a minute or so.

** Navigate to the GOA file that you downloaded previously and click the Import button.  This process should only take a minute or so.

== Exporting a GenMAPP Gene Database (.gdb) ==

== Exporting a GenMAPP Gene Database (.gdb) ==

* Select File > Export to GenMAPP Gene Database...

* Select File > Export to GenMAPP Gene Database...

* Type a name in the Owner field (or else it won't let you export).

* Type a name in the Owner field (or else it won't let you export).